If iTunes can recognize the album in the iTunes Store it can associate downloaded store art with the tracks, and it doesn't even care what format the tracks are in. If you have to add your own art you can't make use of the "downloaded" art system, but must embed it. Only one track of an album needs art for the album to be displayed with art in grid and cover flow views, etc., but during playback on a device, for example, you will probably find that no art is displayed for tracks that don't have embedded artwork. The other main drawback with .wav files is that any information you store about the artist, album, track no. etc. is not preserved in a tag. If you accidentally remove and then try to restore a track all you get is a filename. If you need .wav for compatibility with some other software/hardware then so be it, but otherwise Apple Lossless should provide exactly the same quality of audio reproduction while also supporting tag data and taking up less room.
Sounds like it might not suit you, but others running into this thread might find a use for my ConvertFormat script which can convert selected tracks from one format to another without creating duplicates (the originals are sent to the recycle bin) and preserves playlist membership, ratings etc. (N.b. Converting to and between lossy formats will result in some loss of quality.)