The EXUP is an acronym that Yamaha Motor Co. in Japan says stands for EXhaust Ultimate Powervalve.
It's a butterfly-type valve in the exhaust pipe just before the muffler canister.
It opens and closes according to when the bike's electronics says it should.
The supposed benefit is good low-end power while having good top-end power, too, not trading one to get the other.
The servo motor is an electric motor under the battery that does the opening and closing of the EXUP.
There's a pulley on the servo motor that operates control cables which run to a pulley on the EXUP.
If you remove the stock muffler, the EXUP goes with it since it's welded to the pipe connecting to the muffler can.
Since you're disconnecting the control cables which run from the servo motor to the EXUP in order to remove the muffler, you can also remove the servo motor, too, since it will no longer be needed for anything.
The catch is that unless you do what's called a "servo removal mod", "servo eliminator mod", "servo sub mod", or similarlly-called name which fools the bike into thinking the servo motor is still there, your instrumentation will have an orange Check Engine Light (CEL) light up and annoy you as it tells you the servo motor is now missing.
Read this to learn about the low-buck way of eliminating the servo without the CEL:
https://wr250rforum.forumotion.com/t627-cheapest-diy-servo-bypass?highlight=servo+eliminatorThose are the basics of what's up with the EXUP and servo motor.