Am I going to hit any limitations keeping it like this?
Well, eventually, you will hit the limit of how many files you can have in a Windows file system folder...
If you ever need to look in the windows folder, you will be scrolling for a long time...
I can see no benefit to a flat file organisation over a simple, two level, disc-based folder hierarchy of AlbumArtist\Album\track.wav with one folder per album.
That structure allows you to have a folder.jpg image for each album, and store riplogs for each album, and easily find, move, copy or re-rip any album.
If you wanted to adopt a folder hierarchy, MB can do it for you automatically, using the auto-organise function, using a suitable naming template, assuming your files have correct metadata tags. If they're not tagged properly. MB can be instructed to infer tags from your carefully-formed filenames.
Oh, and yes; convert your files to FLAC. Smaller, better tagging, but still bit-perfect reproduction.