You're correct that there's no significant overhead per-index - 13n entries in one index is more or less equivalent to n entries in 13 indexes. There's a total index count limit of 100, though, so this eats up a fair chunk of your available indexes.
That said, using a ListProperty is definitely a far superior approach from usability and index consumption perspectives. There is, as you supposed, no performance difference between querying a small index and a much larger index, supposing both queries return the same number of rows.
The only reason I can think of for using separate properties is if you knew you only needed to index on certain levels of detail - but that could be accomplished better at insert-time by specifying the levels of detail you want added to the list in the first place.
Note that in either case you only need the indexes if you intend to query the geocell properties in conjunction with a sort order or inequality filter, though - in all other cases, the automatic indexing will suffice.