Sandboxed applications, like Photo Naminator or any other application distributed through the Apple App Store, cannot be passed arbitrary numbers of individual files selected for processing in a single run. The limit is some magic number around 2500 files. Please read Sandboxing and handling many files for more details and how to circumvent this limitation.

For now that's it

So far there are no other known, major limitations. But we'll see as Photo Naminator experiences broader usage.