Well, two reasons:
Wes recently admitted that the Aether saber-rifles were probably aether powered, but the effect they produced wasn't really via aether. Final word hasn't been reached on that level, unfortunately.
Also, aether cancelers don't entirely cancel out aether power systems. It just makes them a lot, lot less effective. Maybe the 'energy blade' effect from the saber-rifle happens to be below that threshold.
One way or the other, we have precedents for aether saber-rifle functioning under aether interdiction. On that level, all I can do is work with what I have - I can't make a claim that it makes sense, true, but I was largely working with this the way I have because of those precedents. It's a bit too late to undo now, seeing as to how the nekomachina have been extensively using the weapons while the canceler was active.
edit: what Kai said also holds up, I guess.