Well I guess it depends on the country in question...
Most countries have very robust systems in place to prevent civilians, paramilitaries, or insurgents from coming anywhere near weapon stockpiles.
Having said that, I read an article just today about an 84 year old nun who has been sentenced to 3 years in jail for breaking into a nuclear weapons complex in Tennessee - considered among the most secure military locations on Earth.
In countries where there is a real threat of organized military groups seizing stockpiles of weapons, I think there'd probably be a number of things a government could and would do to prevent weapons of mass destruction from falling into the wrong hands:
- Basing such complexes in areas of the country that are geographically difficult to attack (i.e. Underground bunkers for example)
- Ensuring these bases are well secured and guarded
- Intercepting and preventing the rise of armed groups and militia in the first place (for example, here in the UK if you decided to start up an armed group, the general consensus is that the security services would get wind of what you've been doing (probably through all the data they have access to), and would try and intercept your plan before you're able to mount any sort of organized armed resistance to the government
- In countries where armed gangs and paramilitaries are a serious threat, I guess it just comes down to firepower and mobility of defense units.
Having enough armed people on the ground to effectively counter any uprising, and to have the necessary means and legitimacy to use deadly force on these paramilitaries.