Previously I mentioned my concern that a drain hole in a battery box was a bad idea, because it would not contain any leaking battery acid.
Searching with Google I found:
The typical battery box serves a number of purposes. In addition to mechanical support, the obvious one is to contain acid and water spills and the nasty damage they can do.
at:
http://www.yandina.com/hints.htm#BatteryBox
This seems to be written in the context of marine applications, where there is something under that battery that could be damaged by leaking battery acid.
So as long as your battery has nothing important under it, like the TM floor, then go ahead a and drill holes in the bottom.
On the other hand, I have rarely seen a battery leak acid.