I've heard that 1.0.2 did improve battery life for some. I didn't see that much difference. However, to answer your question about whether modding can decrease battery life... yes and no.
All of the apps so far, even the most professionally done, are still in the 'experimental' stage. That said, if the app exits without closing up all of its processes then it can cause a decrease in battery life. If it is run multiple times there could be multiple instances of latent processes running. This can be a problem not only with the iPhone but with any OS, and it is not uncommon.
One way to 'clean things up' would be to do a full shut down and restart periodically. It didn't sound like you had pinned the battery drain to any particular app but that could be the case. If you've got the binkit installed you could try running ps or top to see what's running periodically after you've closed things down to see if anything keeps using resources or doesn't terminate correctly.
Hope that helps somewhat.
-KennX