Would it be possible to use FIX IT for hacking a computer (or make it a subskill)? I would rather not use INTRUSION since I don't see hacking as agility based.
To me, it would depend on the archetype and what they were trying to do. If a ninja was trying to break into a building by disabling or hacking the computer system, then I'd allow him to use Intrusion. If the same ninja tried to hack a cyborg's arm or reprogram a deathbot to attack a villain, I'd make him use Fix It, Info/something, or a Knowledge check.
Likewise, if a techie wanted to reprogram the cyborg's arm or the deathbot, he could use Fix It, probably with a bonus even. If he tried the same thing to get into a building, I might allow Fix-It, unless the Ninja was watching, in which case the Ninja would be offended and have to show him how it's really done.
The real question you're dealing with is not which skill to use, but what advances the plot, or makes the plot more interesting?
[color=darkblue]For what it's worth, there are instances in published adventure modules where the author has written things like, "To gain entry, the difficulty of defeating the door's electronic security is a Difficulty of 9 with Fix It, or 8 with Intrusion. It can be broken down with a Strength check Difficulty of 12." So several routes may be viable, just make the Difficulty reflect whatever method you think would work best in a particular situation.