I think the file system issue comes from an error in software raid (as I said, I already have problems with software raid, and most of my files wasn't accessible anymore), or from some bad sectors on disks, I don't think it's an ext3 issue. ext3 is very strong, and each time I had fs errors, it was because one disk was HS. The only other thing that can dammage a ext3 is an unclean shutdown. Well, this is my personnal experience, so maybe others will have different opinion but to conclude, I'd say yes, using software or hardware RAID can make a difference as ext3 relys on the hardware layer (which is emulated by your software RAID in your case)