What size and what speed card do you have?
I have a SanDisk Ultra 128 GB SDXC Class 10 Memory Card up to 80 Mbps. I have 9,000 odd tracks on it, divided alphabetically by artist. One folder for each letter. I have the Tech pack with the MMI Plus.
I did have an issue where I tried to include quite a few playlists on the same card (and with those included I had used up about 100Gb). With the playlists on the same card as the tracks, the playlists worked fine but the MMI wouldn't recognise some of the artist letter folders. I've figured that although the handbook says that the system can handle SD cards up to 128Gb, 9,000 songs AND playlists was a step too far. There are directory limits (from memory 1,000 tracks per folder) but by splitting the artists up by letter I don't get anywhere near that in each artist folder.
I have copied about 1,200 tracks onto the inbuilt jukebox. When I get around to it, I'll buy another identical card for the 2nd SD slot and have only playlists on that: but given that the system allows you to easily search artists or tracks from the existing card and then Play "similar music to" the track you've picked, I haven't missed bespoke playlists at all.