Adding a BTREE
or HASH
index shouldn't break anything, and I imagine that is what you want. At worst you could end up with multiple indexes, or less than optimal ones, which might negatively effect performancewith multiple indexes, or less than optimal ones, which might negatively effect performance. I assume that if you are going to do this you will be evaluating the change to see if it actually does help, rather than hurt.
I guess you could run into trouble with a UNIQUE
index, since WordPress does use a couple of those.