So what you mean is, you copied 10,875 PIRATED ROMS into your HDD?
webMAN games will start to get really slow when you have more than 500 games anyways
homebrew is built with the intention to play backups, not to pirate every possible game on multiple platforms in some sort of ridiculous attempt to turn your PS3 into some kind of super-console that plays every game ever.
If you're a mass pirate, of course it's going to be slow and there will never be any easy way to get around that.
Also, you will always have to figure these things out by yourself because, well... it sounds/appears related to piracy.
My Superslim with 500GB internal works perfectly fine, always has, never gives me problems... Maybe the issue is that you're trying to do WAY TOO MUCH, especially through FTP, something that will wear down your transfer bus and wi-fi processor much faster than standard copies from a USB drive.
FTP is better for large files over 4GB but not more than 10GB and FTP is better to use only when you have to upload 1 thing at a time.
Do what you want but it's dangerous to load your PS3's internal with thousands of games and expect it to last like Raspberry Pi's do. You will end up with soft brick or worse.