Many of the updates would arrive over subspace communications, in the form of software packets. The Enterprise would then replicate the components and the engineering crews would install the updates themselves. In addition to the small replicator alcoves we've seen, the ship should have some large "industrial" size replicators as well. Modifications of this sort can be made without taking the ship off the line. A special repair ship (flying drydock) could be sent forward near the the "front" to keep ships from returning to a starbase. Some changes might require Picard to take the Enterprise to a quiet place, maybe under escort, if major systems need to be off line.
Major structural alterations would still require a starbase layover.
T'Girl
Do they currently use service pack 2 or 3?
