Hacking on the fly can be done in seconds-even in AR. Probing the target takes hours (or days via AR).
And if you've got a good security facility set up, where a hacker cannot access the internal nodes of the building from off-site... then probing doesn't do you much good. And laying inside a secured facility for a couple of hours (in VR) is likely to get you dead. In a combat situation, you don't have the luxury of taking a few hours to hack the opponent's commlinks.
So probing the target, while almost virtually guarenteed to succeed (and unlikely to raise alarms), trades the ease & stealth for time. And probing the target isn't possible at all times.
Hacking on the fly trades quickness for almost guarenteed cybercombat.