Make no mistake, Hitler intended to "ship the Czechs east" when the war ended. He referred to them as "an alien splinter" within Germany, and talked about them in chilling terms as the most patient and intelligent (and therefore most dangerous) of all the Slavs. He didn't trust them even when (especially when) they tried to assimilate into German-speaking society. "That's one of the reasons the Hapsburgs perished. They believed they could solve the problem through kindness."

Hitler intended to allow a small population of "racially valuable" Czechs to remain, but to deport (at best) the vast majority of the Czechs to make room for a new German province.

As for Slovakia, Hitler decided to urge the Slovaks to declare independence because he didn't want the region to be snapped up by Hungary. He didn't annex it because he didn't want to alienate Hungary. It's very likely that after a German victory Slovakia would not have had a long history.