Is there any reason *to* upgrade the biochip in Deus Ex:HR?

No. There are no upsides or benefits to upgrading - at all.

The purpose of this "upgrade" is to allow the Illuminati direct control over everybody with cybernetic augmentations by granting the ability to shut down a users' cybernetics remotely.

Visiting the LIMB clinics to get this upgrade will allow your augmentations (including your HUD) to be disabled, most notably during the Jaron Namir encounter.

The creation of this glitch is what is actually being discussed during the opening scene;

"I have spoken with Montreal. The broadcast satellites are ours when we need them. A few weeks of discomfort, and the public will be primed for our recall."

Additionally, there are several emails that you can find throughout the later stages of the game that discuss the creation of the glitch.

Yes. It prevents the glitch from occurring.