So I am writing up cheat sheets for riggers and hackers and I hit a snag.
So...let's say you have a rigger trying to locate and physically destroy a hacker.
How does the drone/rigger find the hacker?
How does the hacker stop the drone?

Does the hacker have to hack the rigger's comlink, or the drone itself?

This is what the Trace program/action is for.

The rigger or one of his allies has to trace the hacker by finding him on a node and then running Track on him.

The hacker has several options here. If he can find the rigger's commlink, he can hack that directly and attack. He can hack the drone for high-level access and start issuing it commands. If he's had a good look at the rigger's persona he can spoof commands and take control of the drone that way. He can hack the drone and start crashing its programs. He can hack the drone and Edit its incoming sensor information to give false readings. He can shoot the drone.

Couldn't the hacker theoretically create an agent or two to attack both while just running away?

Couldn't both of the PCs create two agents each to attack back?

Why yes, yes they can.

Infinite recursion reached.

As Draco18s said, the Track program is used for a Trace User action, and will likely give you a spot within 50m (expecting the hacker to be using a wireless connection). Could probably narrow this down by having agents in the drones use the Track program when you're homing in to more accurately pinpoint the hacker by triangulation (or more specifically the hacker's commlink); would take three at least to do this with any reasonable accuracy.
Scan to find the node of the drone, Exploit to actually hack it on the fly, and if the rigger is smart Decrypt (among other things usable to protect a drone) to actually log in and be able to do stuff with the drone. Another option is Spoof and pray that the drone isn't currently being occupied by the rigger (i.e., jumped-in). If that fails, upload your skillsoft in firearms and obey one of Murphy's Laws, "When in doubt, empty the magazine."
No, the rigger's commlink need not be hacked, but hacking the rigger's commlink can give the hacker control of all subscribed drones and the rigger's access ID to more easily spoof commands to the rigger's drones that are running on their own.