I thin you can do it as whole. It might just take longer time in the dehydrator.
When you remove the stem, air can get in readily. If your peppers are stored in open ambient, with high humidity, they might get spoiled. But OTOH, if you are going to vacuum pack or grind for powder, stem serves no purpose. An you will have to remove them anyway.

I removed the stems prior to dehydrating to help with the process. As Seysonn said, it helps with air circulation.

I just did a batch of pepper flake last week with several mixed varieties and am very pleased with the result.

A word of caution though, you will want to grind in the garage or outside. I ended up getting a nice puff of powder when I opened my grinder and it was not pleasant!

-Susan

Siouxzn - Good point. I am currently dehydrating to make powder.

I plan on a mix of some Reaper, Naga Morich Jalokia, Choc Scotch Bonnett and Caribbean Red Hab. Prob 85% Hab to 15% Ghost/Reaper.

First time for me..so hopefully it turns out ok.

I definitely do not need a mushroom cloud of that inhabiting the house. Might be grounds for divorce...