This has worried me from the beginning, because true optimal play will require that you waste time on boring activities, and it's a rare case where I've not fully addressed it. The current system exists as it does because I want it to be a highly flexible tool, and it is, but with that flexibility comes a greater chance for abuse.
Note that the hacking system is still incomplete and I have also wanted to explore solutions for these issues for a while now, it's just not high on the list of priorities at the moment.
Regarding reconnects, there is actually a mechanic at work that I attempted to use in preventing optimal time-consuming strategies: Every time you are detected and then reconnect to the same terminal, even after it is no longer tracing, your chances of detection go up incrementally because you've hacked there before. So it actually gets progressively more difficult to hack the same machine. I think making this more apparent, as well as incrementally increasing the difficulty of the hacks themselves (something I thought might be going to far), will be a simple and effective way to prevent single machines from being overly useful. (I should also remove the cap--right now I've capped the maximum number of connects that will affect the detection rate.)
That particular change doesn't cover the swapping issue, though.
I have considered for a long while the possibility of getting rid of hackware as it currently exists. Having it work from the inventory would go against the general principles of the core mechanic, however, and is something I'd like to avoid. (I'd make an exception if inventory space was truly limited, but we don't really want to do that.)
What about making collected hackware a permanent part of your core? That's one option I've mulled over since its inception, though it would require making these components even more rare and difficult to acquire. This also goes against the core mechanic, but in the interest of steamlining we do need to take some action.
To throw another wild idea out there: What about making them permanently occupy a slot, but be impossible to lose?
What I really wanted was for hackware to actually require a slot, but hoped that the player would keep it attached rather than always swapping it out. That's a poor expectation since they do little for you in combat, although that
has been changing over time, and will become a more important aspect as the world grows and you may be fighting alongside allies more often. Multiple types of hackware aids in certain combat situations.
To specifically address the other two comments:
1) Don't make me wait.
Waiting for any reason is supposed to work against you in its own right, and it generally did a very good job of this before when there were many more hostiles. Since Alpha 1 the game has become significantly easier, however, and that combined with players' higher skill levels means you may not mind waiting around longer even if it means a few more encounters. This will sway back in the other direction a little bit in Alpha 5 because I've halved the effect of Alert(Purge).
2) Don't make me scroll.
This will be addressed with the alternative inventory management interface discussed previously (not sure if you've seen that one), which will apply to more than just hacking, but large inventories in general. (Alpha 5 also further increases the mass of Lrg./Hcp. Storage Units beyond proportionality with Sml./Med. units.)
Cogmind: *Shoot terminal*