I can give a partial answer based, not on "what Hitler thought", but what Nazi German policy was towards the various Yugoslav peoples. "Nazi German policy" here means both Nazi ideology and German grand strategy -- the two sometimes went together, and sometimes not.

One thing to start with: While Nazi ideology was brutally racist at all times, it wasn't always consistent. And sometimes it allowed for the idea of "good" Slavs -- or, at least, useful Slavs who didn't need to be oppressed, enslaved, or exterminated. The Slavs in question were always small, non-threatening groups that had a historically positive relationship with their Germany neighbors. Again, the word to note here is "inconsistent", and the actual history gets quite complicated. That said, we can do a quick survey of the particular Yugoslav groups.

Slovenes -- Nazi policy was that the Slovenes were natural allies of the Germans. Indeed, some Nazis held the position that Slovenes were Germans -- confused Austrian Germans who had somehow become "Slavicized". Other Nazis held that the Slovenes were Slavs, but were analogous to "good" Slavs like the Wends and the Sorbs -- small Slavic minorities that lived in southeastern Germany. Either way, it certainly helped that the Slovenes were perceived as the most "loyal" of the Slavic groups that had existed within the old Austro-Hungarian empire. They had kept their own language, and pushed for some local autonomy, but they were never perceived as threatening or potentially separatist the way that, say, the Czechs or Serbs were.

So, much of Slovenia was incorporated into Germany -- Germany actually had a bit of Adriatic coastline for a few years! -- and Slovenes were, in 1941-3, treated little worse than Germans in Germany. In the last year of the war this broke down somewhat as resistance mounted, but that's its own story. Meanwhile, it's entirely possible that ideology may have bent to serve strategy here: the Germans wanted an outlet on the Adriatic, and annexing Slovenia meant either ethnically cleansing the Slovenes or somehow defining them as acceptable citizens of the Reich.

Croatia -- Nazi ideology held that Yugoslavia was an artificial state created by Serbian annexation of the former Austrian territories of Bosnia, Croatia and Slovenia. In this view, the Serbs were the villains, while the Croats, Slovenes and Bosniaks were their victims.

Again, this view was influenced by Austro-Hungarian experience. The Croats had been mostly pretty loyal to Austria; in 1848 they had helped save the Empire from the Hungarian rebels, and in 1914-18 they had fought loyally and long for the Emperor, only abandoning the Hapsburg cause in the last few weeks of the war. So, while Croats weren't viewed as near-German Good Slavs like the Slovenes, they were broadly seen as Okay Slavs or at least Useful Slavs.

Creating a puppet Croatia was actually a clever stroke on Hitler's part (though it was a nightmare for everyone else involved). An independent Croatia would be totally reliant on Germany. To the south, Mussolini wanted all the Adriatic coastline. To the north, Hungary dreamed of recreating the "Lands of the Crown of St. Stephen", a Greater Hungary that would of course include Croatia. And Croatia itself included large non-Croat minorities that were ambivalent or hostile about being part of Pavelic's Croatia. So, Croatia literally had no choice but to be a German puppet state. Of course, it didn't hurt that Pavelic himself was a cruel and viciously racist thug who was all-in for ethnic cleansing and genocide. Other than his Catholicism, there wasn't much to distinguish Pavelic from the Nazis, and even his Catholicism was of a sort that just made him more anti-Communist and anti-Semitic. So, he was generally quite happy to follow the Nazi lead.

So, Hitler allowed Croatia to exist as a puppet state because it made good sense for Hitler: puppet Croatia was a small friendly state that provided modest but useful contributions of men and resources to the Nazi war effort.

Bosniaks -- Again, you want to look back to the Austrian experience. The Bosniaks had fallen under Austrian rule in 1877 and stayed there until 1918. They weren't too happy about it at first, but the Austrian authorities very cleverly left the Bosniak's property, religion, and social position mostly untouched (while driving out the actual Turks).

Now, in late Ottoman Bosnia, the Turks were the rulers; Serbs and Croats were mostly peasants and artisans; Jews were merchants; and the Bosniaks were the landowners and filled the professional / educated classes (doctors, lawyers, bankers, etc.). The Austrians left this system mostly intact. So within a few years, the Bosniaks realized that they actually had a pretty good deal, and also that the Ottomans weren't coming back any time soon. So they switched their loyalty from the Sultan to the Emperor and served him loyally until the Empire collapsed.

Under the Kingdom of Yugoslavia, the Bosniak position tended to deteriorate. The Kingdom was dominated by Serbs, who tended to view the Bosniaks as historical turncoats, and also to resent the fact that -- in Bosnia -- they controlled most of the land and shared the economic high ground with the Jews. The Croats weren't big fans of the Bosniaks either -- why would they be? So while there wasn't persecution as such, there was definitely a fair amount of anti-Bosniak prejudice and de facto anti-Bosniak policy. In particular, Royalist Yugoslavia looked for ways to break up the big Bosnian estates and distribute those lands to the Serb and Croat peasants. So the Bosniaks were a lot less loyal to Yugoslavia than they had been to Austria-Hungary. Also, as big landowners they tended to be fiercely anti-Communist.

Then after 1941 -- well, again the Bosniaks were a group that were potentially useful to the Germans. Pavelic's natural instinct was to (of course) persecute, dispossess, and eventually murder them. The Germans weren't having any of that. In a way, just as the Germans kept Hungary from grabbing more of Croatia, they kept Croatia from persecuting the Bosniaks. (One interesting side effect: Croat nationalism came up with a theory that Bosniaks were confused Croats who had converted to Islam!)

Anyway, the upshot was that yes, the Bosniaks were mostly allowed to live their lives normally, or as normally as anyone did in the Balkans between 1941 and 1944. They were anti-Communist, reasonably loyal, and modestly useful.

Serbs -- I am emphasizing Nazi ideology and German grand strategy more than "what Hitler thought". But in the case of the Serbs, it is probably relevant that Hitler was Austrian. Serbs occupied a special place in Austro-Hungarian demonology: basically, Serbs were the troublemakers who ruined everything. It was a Serb who started WWI by assassinating Archduke Franz Josef, driven by Serbian expansionism and greed for Austrian territory. Then the Serbs humiliated Austria in the first weeks of the war. Then they further disrupted Austria's war plans by fighting ferociously for a year and a half, until the Austrian war effort on that front had to be bailed out by the Germans. And then, finally, it was the Serbs who turned the previously loyal Croats and Slovenes against the Emperor, to create the ridiculous "Kingdom of Yugoslavia". Austrian patriots might resent the Italian treachery or the Romanian backstab. But those were at least real countries. Serbia was a nonsensical little comic-opera parody of a state that somehow, somehow ended up grabbing more Habsburg territory than anyone else.

Nazi ideology pretty much adopted this Austrian point of view: Serbs were, most definitely, Bad Slavs. And the Serbs were also blamed for starting the war in the Balkans in 1941, by overthrowing Prince Paul's government. So, they were marked for oppression within occupied Serbia, and dispossession, ethnic cleansing and genocide within puppet Croatia.

There's much more to be said, but this is already long. I hope this is a useful partial answer.

Hi there,

On /r/AskHistorians we often get questions along the lines of 'what did Hitler think about X' - I mean, as an April Fools joke one year, we changed the sub to /r/AskAboutHitler. However, for better or worse, many of these questions about what Hitler thought are, in the literal sense, unanswerable. We don't know what Hitler thought about many things, and especially about things that were inconsequential for him. Hitler did not keep a diary, and the collections of his private conversations are disjointed and nowhere near complete, being almost completely dependent on the post-war recollection of his intimates (who may also be unreliable in their recollections, especially given those circumstances).

Of course, you may still get an answer to this particular question! However, broadly speaking, proving the negative is very hard (there could be a 1965 article on the topic in Swahili), and if you've asked a question which is almost certainly "We don't know, and he probably didn't care anyway", few historians familiar with the topic matter actually are going to want to put in the necessary gruntwork, doubly so about a man who on a personal level was decidedly uninteresting.

For more information that will be helpful in understanding the context around your question, please read /u/commiespaceinvader's wonderful post on why Hitler's opinions actually aren't that interesting, and please see here for an example of a historian attempting to find evidence about Hitler's thoughts on a topic, but finding that it is likely unanswerable.