Would rare (less than 50,000) weapons such as the ones listed be issued to one group of soilders, or spread thin? How was it decided who would get them?
I'm most interested in the Nambu Type 100, but if information on that specific weapon isn't plentiful than the general trend for rare weapons will work.
I can't speak for the Type 100, but I can talk about the MKB 42 and the STG 44 for the Germans.
Initially the MKB 42, which is a very early version of the STG 44, was only produced for a short time and only 12,000 were made. Because of the nature of the project, being early in it's development and just now in 1942 being put into service, were sent to whole units in the eastern front for trials.
From the trials it was determined that the MKB 42 was not going to replace the K98, but instead was going to support it in combat. Meaning that it would be issued specially to troops.
Once the MKB 42 was renamed the MP 43 in 1943 and upgraded a bit, the first productions of these went to the Waffen-SS, and then specially to the 93rd Infantry Division.
In 1944 once renamed the STG 44, and improved, the new run was selected to go to the 1st Infantry Division of Army Group South and 32nd Infantry Division of Army Group North. But was only fully equiped by the 1st infantry. The first infantry completely replaced all of it's K98s with STGs.
Special weapons like this were also given priority to elite units, like the more elite Waffen-SS units like SS-Leibstandarte, SS-Panzer-Division Das Reich, 3rd Totenkopf, 5th Wiking, the 12th Hitler Jugend. As well as the regular armies elite units like Grossdeutschland.
Later in the war with the creation of Volksgrenadier divisions, STGs where issued as support weapons like they had been initially meant to be.
So to then answer the question fully, these weapons were issued on the Division level, especially to elite units who could use them more effectively. Spreading them thinly, especially new weapons that required different types of ammo would have been a resupply nightmare had they only been issued to select few across entire armies.
Sources for you: http://sadefensejournal.com/wp/?p=2087&page=2
http://www.efour4ever.com/stg44.htm
http://www.lexikon-der-wehrmacht.de/Waffen/sturmgewehre.htm (This one is in German, sorry.)
/u/jareds011 has already answered for the MKB 42. As for the type 100 and Avt-40: Would it be more likely that the type 100 would be spread more thin because it uses a round that was also used by the Nambu pistol? And for the AVT-40, it uses a very common round used by the Russian military at the time and used the same magazine as the SVT-40, would that further increase the likelihood that it was spread thin?