I'm sure some people have looked at this and decided that the cost/benefit ratio doesn't justify the massive investment that would be required to address the possible issues. I'd also guess that people who might be able to spoof these systems have concluded that there are cheaper and more dramatic ways to kill people. The object of terrorism is to use dramatic acts to promote a cause. Deaths which might well be mistaken for equipment malfunction or pilot error and would depend on the terrorists being able to claim undeniable credit just don't do the trick.
Besides, you're asking a bunch of professional pilots whose whole job is to be fully aware of the developing situation to blindly follow your spoofed electronic guidance without cross-checking other inputs available to them. They are trained to recognize a bad ILS signal (e.g. wrong rate of descent from known waypoints), incorrect VOR, etc. Only the TCAS scenario really works in my mind, and only if ATC has already established a context in which the false warning would make sense to the pilot. Trying to use TCAS to get a pilot to fly into the ground or another aircraft would be pretty tough. Actually I think, given last week's near-collision at JFK, that hijacking a tower or ground controller's frequency could be more deadly.
Hollywood might buy your plot for the next edition of the "Die Hard" series but I think the bad guys have more faith in proven technology like underpants bombs.