Mac OS X file system and tagging question
No, I don't think so.  Spotlight indexes files in order for quick searching.  Once indexed, a file is very quick to find, the part that takes time is the actual indexing.  I suppose you could argue that the act of moving a file might cause it to be re-indexed (now that it's in a new location), but I don't know enough about how Spotlight works to be sure.  Either way, the difference you would notice would be minimal.  Once the initial indexing is done, the time spent adjusting the indexes is not big.