I don't think so, at least not any more: I've tested locked files and they work fine. Are you certain? Is it when the files are deleted?
Basically, I know of no problem like this in the current version. Note that locked symlinks -- one of those things that can't be done in Unix, but can with Finder -- can cause issues, but we have that logged and fixed internally. But this doesn't sound like that case...
Here's what I've tried:
- Create a file (various types, including XML, but that doesn't matter)
- Lock in Finder
- Copy to a destination
- Smart Update (no problem - no changes)
- Unlocked file and modified
- Smart Update (no problem, copy unlocked)
- Locked file
- Smart Update (no problem, copy locked)
- Unlocked file, modified, re-locked
- Smart Update (no problem, modified file copied, locked)