I can believe that NTFS is slower than most Linux filesystems, though I'd be curious how much of that relates to things like use of ACLs, etc. Regardless, both security-related and filesystem-related speed differences on developer systems should be effectively negligible except in edge cases.

If filesystem differences are making a significant difference, it's time for someone to suck it up and spend a few hundred dollars on SSDs for the developers (and not the cheapest ones available, which frequently lack DRAM and can have their own speed issues).