I have done it many times and it is a pain to remove the carb but I still do it because the space is extremely limited if you do it on the bike. You would have to remove the throttle cables to rotate the carb anyway.
Hmm, I'm experiencing the same thing on my 2003 drz400s. I pulled the carb and cleaned everything and it starts immediately when is cold but don't restart after it is warmed up unless I let it sit for a few minutes. I have not checked the valves.