There shouldn't be any security risk from keeping the files. Worst someone might be able to find out what MODs you have installed. On the chance that there is a vulnerability in one of those MODs, that could be problematic.
YOu could set a .htaccess "deny" directive on the /store/mods/ directory. This would not affect AutoMOD's ability to work, but would prevent anyone accessing the files.
A Donut's Blog
"Bach's Prelude (Cello Suite No. 1) is driving Indiana country roads in Autumn" - Ann Kish