Even though You Thought Points are originated from the You Can Think Pad, the Player cannot earn points in this device as its purpose was changed when this system was first implemented.
The acronym "YTPs" might be a reference to YouTube Poop, the infamous video mashups in the YouTube web containing edited pre-existing media sources for humorous, obscene, annoying, confusing, shocking, détournement, or dramatic purposes.
Furthermore, many people thought the name "YTPs" actually stood for YouTube Poops, and so the actual name may be a jab at that.
Baldi's Basics Plus
Prior to V0.2, there were two ways to lose You Thought Points: Baldi catches the Player without An Apple for Baldi and bringing the wrong Number Balloon into the Math Machine.
Before the V1.2 update, these values used to be only for placeholders because the methods were not implemented, so they always show up the same values. As of the V1.2 update, they have added a working counter and the Player can earn YTPs in multiple places.