Given that you're talking about "quite a few" folders, I think it'd be good to check up on the theoretical and practical limits for your filesystem of choice, though - ext2 for example starts getting noticeably slower when you have a lot more than 10.000 entries in the same directory. One way of getting around that would be segmenting your database names in blocks of three or so (so "database" would be stored under dat/aba/se/<datafiles>). Takes a bit of management, but then you already have something in place to create the symlinks anyway.
Also, as a matter of manageability, I'd not put your real database dirs somwhere where there is other stuff - make a separate directory and keep them all there. Another point of note, but I suppose you already know that, is that this will not work with InnoDB unless you have the file-per-table option enabled. -- Bier met grenadyn Is als mosterd by den wyn Sy die't drinkt, is eene kwezel Hy die't drinkt, is ras een ezel