I like to strip out any "keeper" seeds prior to drying... I have a very basic dehydrator that doesnt have temp control, so I dont want to risk damaging them. It does a great job for my needs.
As someone else mentioned, if you are drying hotter peppers, the bitterness from the seeds is not overly noticeable in most cases. I tend to save as many as I can as I find it can add a bit of a "nutty" flavour to the powder that I like.
I cut my peppers in half before drying. A few taps will generally shake out most of the unwanted seeds once the pods have been thoroughly dried.