Got a desktop in a tower case, USB connectors on the back plate( | | ) have no "top"
The "top" is the side furthest from the motherboard.
Interesting, is this a universal thing?
It was the plan, and the most common result. But no, it isn't universal. For one, not all usb cables even include a logo or marking for the top of the cable.
You can, with a cable, rotate it another 90 degrees and visually identify the top.
where i paint over with bright nail polish to make it easier to see (and also have seen the usb symbol on the wrong side)
This depends on the machine! But for a given machine, the logo should be oriented the same way for all cables, at least.