Just had a 40 degree temp drop here in the lovely South. Bottomed out my Magura Thor for the first time since its purchase... ehh like 6 months ago? on about a 3 foot jump. Do I need to air it up because of the temp, or go ahead and service it?

Dunno about the Thor, but that shouldn't be much of an issue... a few psi perhaps.

Have you checked the pressure on the fork since you bought it? Set it up correctly when you first got it?

I always check air pressure on both shock and fork on my bikes every month. Just a maintenance thing I do.