Hackers are designed to be resource-light, so the character will have backup skills. On top of that, the system bends over backwards to make sure there are times when you have to physically enter a location. The PC should have other skills to fall back on if they don't want to get hosed.

Things that would be extended actions that would eat up lots of table time should be abstracted to simple skill roles. Just make it so that in your world, most devices count on limited accessibility over IC for protection. If you can only hack the elevator is from a terminal inside of it, you both give a reason for the hacker to physically tag along, and a reason to avoid adding complications. (Although alerts being raised and ensuing complications are a fair cost for failing.)

Extended solo hackfests should be treated like extended solo metaplanar quests, or indeed any extended solo character arc. Do it over email, or some similar way of resolving things between game sessions.