I'm starting an SR3 game, and one of my players has mentioned playing a shaman-decker. I've combed through the rulebook, and cannot find actual rules for differences in capability between a trodes headset and datajack. Am I just overlooking something?

A datajack gives you a simple, solid, reliable and trustworthy data connection.
A trode net is a flimsy, faffy, and awkward set of electrodes to painstakingly apply over the head that are easy to disrupt, catch, tweak or move.

Technically both will let you do stuff in the matrix, or control actions for a magic user on a technical device without need a datajack and losing a whole point of essence or taking a geas. But while you can go leaping into a car, grab the datajack and ram it into the slot, and then be driving via a virtual dashboard, that's not going to happen with a trode net - you need minutes to carefully arrange that over your head and strap it in place, positioned carefully in just the right position to pick up the right bits of brain activity. It's not anywhere near as quick, and to do it you'd better hope you don't have a pink mohawk or a massive afro... Or that you're not in the middle of a combat situation and worried about taking your head armour off.

TLDR - mostly in terms of speed of preparation to do the thing, rather than speed of actually doing the thing. It will slow down their response to being able to quickly do something, but it shouldn't be insurmountable. It can be used to add narrative tension or flavour to your game, or you may at times just handwave it as "well, as you're not used to the faff of sorting your trode-net out, you managed to get online in 3 minutes compared to the normal 4...

It depends. If for whatever reason you're playing core book only or otherwise not using Matrix, the answer is not really.

If you are using Matrix, the calculus changes. Check page 18—trodes take 3 combat turns to fit on one's head, they halve the user's matrix reaction (round down, minimum of 1) and cap Initiative dice at a maximum of 2d6, and they don't permit the use of Pure DNI which means leaving a bonus +2+1d6 on the table.

But it turns out you can still run hot ASIST which gets you your Hacking Pool, so it's mostly a crippling disadvantage in cybercombat specifically, which is something you generally want to avoid until you get to higher levels of matrix play with fancier decks and programs and whatnot.

~J