I just finished rebuilding the last six thru-hulls on Anthem last summer. I had to because of what the "professionals" had done previously. I'd suggest that the most important factors may not be time or money.

First of all, here's the best site I've seen on thru-hulls. Props to Mainesail. http://www.pbase.com/mainecruising/seacock_primer

Regardless of what you decide, educate yourself so that either you can do the gig or you can make sure someone else does it right. You don't provide much in the way of specifics but there's a difference between thru-hulls and seacocks. If you have valves screwed onto the actual thru-hull (mushroom) DO NOT simply replace it. The mismatch in threads (tapered/straight) means there will be only two or three threads holding the whole affair together. I about crapped my pants when I found out what was installed by people who should've known better.

It ain't rocket science but it is dirty, sweaty and tedious. As the others have said, most of the work is getting access (I rebuilt quite a bit of cabinetry.) The real craftsmen will charge a fortune. For $300 a pop it'll be the minimum-wage dude lowest on the yard totem-pole who ends up doing the work.