I think that's a legacy from MacOS Classic, where there was a way of keeping a handle to a file that was independent of the file's name (so you'd still point at the same file even if it was renamed).
You might find the file handle stuff comes from the fact that a lot of the Be employees were originally Mac developers at the start, and quite possibly because they wanted to support some of the features that were in the OFS (original File System, the Database like file system BeOS originally shipped with right up to the AA/PR1 releases. DR8.x definitely had the old file system.)
I remember reading some BeOS API documentation where it said something like "paths are UNIX-like, entry_refs are MacOS-like and they each have some pros and cons". Can't find it now, though…
