Possible other drawback/advantage. Many/most cell phones these days have GPS tracking systems in them. Good for tracking your enemies, bad for when you want to stay hidden.
Exactly. If the Yeerks can track email (#20, from David's computer) and bring down Visser Three and an army of Hork-Bajir in a manner of minutes, imagine how much more of a security risk it'd be if the Animorphs could be tracked via GPS (especially in #49 when their secrets were blown). I suppose they could always purchase prepaid phones for mission use only and then discard them right after. However, the Animorphs were often short on cash, and this probably couldn't have been done more than a few times.
On the plus side, like you said, it'd be useful to track controllers (i.e. Chapman) to find secret locations to the Yeerk Pool, without having to follow them everywhere. I'm sure Ax could find some way to hack into the network and use it against them. If not Ax, then even Erek could help out with that (It probably would give the Chee a bit more to do in the series, tracking down known locations throughout the city).
Something else: with the update to modern times, there'd also be a higher risk for them to finding secluded spots to morph. Think of how many cameras there are everywhere you go: traffic lights, atms, security cams, etc. Plus, there are all those motion sensitive alarms in nearly every store now. It'd be damn hard to sneak in anywhere if they tried to do some those things now.