How do you fixed yours?
Here how it looked.
Didn't get any notice to delete
That doesn't show me that you installed 250 themes.
I fixed mine because upon booting into the system menu, the 3DS itself told me to delete until I had 100 or less on there.
If that is indeed your issue, go to System Settings->Data Management->Themes (should be accurate). Delete them until there are 100 or less. The limit is 100 and your home menu won't function properly with more than 100 on there.
I just noticed your update. Ok awesome. As for the other fix attempt, you can use FBI to delete the .bin file in hblauncher folder. Then, as long as your 3DS is connected to WiFi, launch Homebrew Launcher from the home menu. Perhaps your payload got corrupted.