Needs either an unlock signal, or a dead man's switch that holds a lock shut. In either case, subject to jamming.
If a unlock signal is jammed, foreign powers can disarm your forces. Therefore it's a dead man's switch. This means rebels can put up sovereignty umbrellas. Therefore, locks only make rebellion more expensive, hardly impossible.
Still, front door locks don't make breaking in impossible, merely harder, and they're cost-effective. Perhaps the crypto-lock can use tricks to make it worse, like sharing a channel with radio chatter, meaning jamming the switch also jams your own comms.
There's an issue with small arms. They aren't hard to make yourself. Still, an M16 is not basement forge tech, and it puts up another couple barriers to rebellion. Also miniaturizing the locks to that extent greatly increases the malfunction risk, and the last thing you need is less reliable M16s. You can still lock the armoury door, though. Having a chance to shoot the rebels while they're jimmying the lock can make all the difference.
Futher, the actual trouble with locking small arms is a side issue when modern destruction is mainly wrought by planes and howitzers. If you can't win against a rebel army lacking artillery, then you richly deserve to lose. Even if it gives their heavy guns reliability issues, it will be cost-effective. The loyalists can destroy the gun, or destroy the jammer. This additional option would help tremendously in a real firefight.
There's also the issue that jammers can't, by definition, be hidden. If they're working they can be triangulated and targetted. This is perhaps a reason to avoid fibre optic lines, even though their jam-analogue is harder to effect.
Finally, a ruler can take the spirit of crypto-locks and run with it. Adding several layers of technological replacements for warm fuzzies would have multiplicative effectiveness.