There was a gadget installed on my Corolla when I purchased it new, presumably by the Toyota dealer. Not a tracking device, but some kind of connector-keyed-inter-lock that prevented cranking. Installed on the lower dash panel, right above the driver’s knee. Pretty much invisible unless you knew where to look. Which I didn’t. Probably used to prevent car-theft from their lot. They removed part of it after purchase, but left part installed, which I knew nothing about. And the part they left caused me grief a few years later, as I apparently hit it with my knee one time and cracked it, and then my car wouldn’t crank intermittently. I finally found it by tracing out the wiring, comparing to the shop manual wiring diagram, until I found that some gadget was wired in the cranking circuit that didn’t appear in the shop manual.
So I concur with the OP, good idea to remove it.
First thing you have to do is find it. It makes a beeping sound you say? That’s generous of them to provide a covert devise with a beeping sound. So when it does beeps, pull over, and see if you can find where it is by sonic-location. Then, to get some advice how to remove it, take some photos of it and how it is wired up, and post them here.