I absolutely love the idea of hacking. This mod scratches an itch I've been having since I started SE; the ability to hack the cargo ships (arrr ima purrate m80). The only downside is that it has to be your computer built (or otherwise connected to) the enemy ship wanted for hacking. Merge blocks are a common suggestion for this, but by the time I've built a merge block on the enemy ship, either I'm dead or my ship is in bits.
So, people have suggested ranged hacking, but like you've said, there's balancing issues.
After all, if you could easily hack into everyone else's ship from afar, boom, game over.

But, you don't see Anonymous walking into Sony and plugging a virus right in. So, how could the hacking be ranged, without balance upset?
My idea: Two blocks for ranged hacking. One, a specialised antenna(?) that adds the ranged effect to the computer. Required to be outside the ship. More antennas could mean more range. They would require some/a nice chunk of power (could just use the base game antenna). The second, the actual computer. Would require lots of power (you're attempting to hack the enemy's systems, through any firewall/defense mechanisms, without a physical link). Could be scalable (more computers = more hacking power)
The difference from the normal computer; more computers doesn't mean more possible blocks hacked. This system of one computer per block would be replaced with a "difficulty" sort of system. Again, you're breaking firewalls and other defenses. Assuming that we're this far into the future, the firewall or whatever defenses are on the enemy ship would (probably) be self-healing (I.e., actively scans for any sort of breach of security, then repairs that breach). Because of this, if the computer power was low, it would not have the speed to break the firewall and then hack the block. However, because the firewall would have to scan each part of itself, there would be a chance the computer would get lucky and hack a block despite being slower.
So, for example, one computer would have a 1% chance of success, add another and it doubles, 2%, another, 4%, etc. Of course, more power consumption would come from this.

TL;DR
For ranged hacking, replace the one comp-per-block system with a success chance system focused on one block at a time. More computers equals more success chance, not more possible blocks. More computers also equals more power consumption.

Of course, this still presents some balancing issues (large reactor, bunch of computers). Maybe some form of defense block could be added as well, I'm not sure.

Let me know what you think of this idea (or if I should clarify more XD).