I know what you mean, but I think the most common/practical approach to storing your music online is an /Album/Artist/Track directory hierarchy. It's easier to manage from a human standpoint and probably easier for some software to deal with. In that case, the identical names shouldn't become an issue.
Squeezebox/Logitech Media Server has some provision for all artwork to be stored in a common folder with some kind of name tying it back to the music, but that sounds like a nightmare to me!
I have a large libraries of ALAC,FLAC, DSD, and AAC tracks. I keep my music drive organized pretty much exactly as you describe (except the AAC and ALAC have their own root directories based on their iTunes libs). This turns out to be important for managing across multiple players.
But I still find that any album-art scheme that is used instead of just embedding the art in the files using tags to be inferior for a couple of reasons. Yes - you eat a bit more space by having the art embedded in each track - BUT
1) I found bugs all over the place in mixed-album playlist rendering in multiple players.
2) God help you if you use more than one player and they use differing non-embedded album-art schemes. I use JRiver for playback on my main AV system, Logitech Media Server for playback on my squeezebox-duet-based screened porch system, and then I have two hot-rodded (240GB) iPod classics for the cars and a Fiio X5 portable DAP for other mobile uses. The combined support on these systems for folder-based cover art is error-prone and sometimes buggy. Yet they all deal perfectly with embedded album-art.
If you are already going to the trouble to rip titles for playback, it is one small extra chunk of workflow to find and download the art (which you can do while the disc is ripping), go into your favorite tool, highlight/multi-select all of the tracks to which that art applies, and embed it. It will then display properly just-about everywhere, including most near-future players that you don't yet have, with minimum of muss-and-fuss when you are done. You can do this when you are cleaning up the other tags - filling in blanks, correcting errors, and (if you are inclined as I am) setting the genre where YOU think it belongs ;-) In general, if you make a short investment at the end of each rip in ensuring that the most important tags, including album art, are accurate and complete then it comes back to benefit you in multiple ways later.
If you want it to be really easy and are willing to pay - get something like PerfectTunes (there are other excellent tools too - some free). I happen to be partial to PerfectTunes because it has the added benefit of making a pretty large collection of high-quality, higher-resolution (1400x1400) art available from their own servers in addition to searching other internet sources for it. It can also do large batch jobs on your entire library like "find all the low-res art and suggest replacement art" or "find all the tracks in my lib that have no embedded art and suggest art". You can then review/revise the suggestions and then "apply all" and the entire library gets cleaned up in one shot. I found it extremely useful in overcoming "technical debt" of a large library that I had previously not been consistent in handling.