Long term, not entirely too much. There is a theory that overclocking too high can cause issues to your CPU with the heat but that is why the devs will always make it known what is stable.
The thing that is making me 50/50 on rooting this is the idea of having to maintain my phone based on dev's making updates. A way I look at custom ROMS is that they're always in Beta. In all the different ones I ran on my Eris there was almost always some type of update 1-2 times a month due to something being broken. The only one I didn't this happening on too frequently was Cyanogen based ROMS but again, there were still some issues.
Some of the common things I've seen come up with most ROMS with issues are:
Antenna issues
Wifi
GPS
Not receiving MMS properly
Front facing camera
4G
Despite the above listed, also keep in mind these things also happen on vendor released phones. So yeah, if you do it have fun it can be a lot of fun but don't expect near flawless ROMS