Has anyone seen a development hindrance when placing a prospect on inactive when their stamina dips low??? Any thoughts/ideas?

No one can answer the first question with any certainty.   You can't notice something that isn't there(lack of development).

My standard practice is to deactivate players when they dip below 98%.    I've noticed that many minor league injuries happen at 97% or less.   Obviously a small sample size but it seems to be more than a coincidence.  My players seem to develop just fine using this system.

I never thought about it, figured you'd be alright unless you forget the player and leave him inactive for a month.