the reason for the 99 files per folder thing came from firmware version 9.0.43 for a player made by MayIce Technology, a 1.5" screen 2GB player. There was a bug in the firmware that caused the player to crash if you copied more then 99 files in a folder.
They fixed the problem but the 99 files per folder rule stayed around. It really depends on your player. I have several players. On one I have 155 files in one folder with no problems. But I have another player that can only hold 47 files and i start to get reboot problems. its either the firmware or an issue with the sectors and waffers on the chip.
Experiment with you player and see how it goes.
Here's a thread about playlists thats really helpful:
http://mympxplayer.org/playlists-vt1...light=playlist