I think the most likely reason is that they probably just didn't think of linking Data to the ship wirelessly. We'd have it as a given now, because we have phones that actually fit in our pockets (and aren't the size of a brick), WiFi, Bluetooth, NFC or lots and lots of wireless sensors (Zigbee etc). When the show was originally written, digital mobile phone standards were still a work in progress. I think the mobile phone revolution of the 1990's helped to visualise what would be possible in the future. What did the writers have to play with? Analogue mobile phones or CB radio, perhaps?
They seemed to have anticipated a return to a more centralised vision of computing, and considering the cloud era (I dislike that word, but anyways) we're in they may not have been entirely off the mark. In retrospect, it seemed like that was a totally solved problem for them and it didn't seem to be an issue worthy of debate. A wasted opportunity, imho.
Who knows? Data might have been a special case. Not many Soong-type androids were ever built and I'd guess his architecture (for lack of a better word) may have been totally different to anything else in the Federation. Which meant that without special efforts from Geordi or Data, he may not have been able to connect to the ship without serious engineering and/or ingenuity. For example, see the picture of Data's head I posted earlier.
I think that we might sometimes forget that TNG is close to thirty years old, and that the writers were writing for the time and the world they were in.
And lets face it - even if they did think of that, they'd have to make sure that Data couldn't just wirelessly link to the ship and turn off the busted valve/forcefield/fire/etcetera right in front of them with a mere thought. Like all of the other times they have to conveniently disable the communications, replicators, transporters, life support or engines for the sake of the plot.
But as you and other posters have said, the writers for that show had mobile phones and wireless computers to base their world off whereas the TNG writers were only on the cusp of those technologies.
If it was written now, Geordi would probably design a quantum device that Data could access a specific terminal (with human user level access) that worked over subspace, leading to some good twists on the whole "aliens have taken over the ship with forcefields/transporters/biological weapons"-type scenarios.
Data could be away planet-side or on a shuttle and eventually figure out that his access is to the main ship systems are blocked due to a hijack and then work out something with an environmental control bypass or something.