As an avid SBH player the best way to counter them is mines. On flying maps mine ramps to the top of buildings, 3 should be plenty because if I run through those mines (and maybe survive) I will have low health and can be killed fast. Further more if you even THINK you walked past an SBH just fire a clip around until you hit something, then follow that something. Most new SBH players will instantly start attacking you, other more experianced ones will try to juke you so be aware of it.
And to be frank I find SBH+Nuke is one of Nods staple strats since GDI's vehicles are much more powerful then Nods and can take a much larger beating. It's an interesting balance mechanic I feel.
Edit: Forgot to add that in original ren placing a nuke beacon meant the entire group of defenders on an enemy team would fan out, the one who found it would spam "defend the [structure]" and the rest would swarm it. Forced some clever nuke placements, but on large pop servers it became extremely difficult to get one off.
It's mainly a matter of most new players learning how to react when they hear "Nuclear Strike beacon deployed."
Also you can hear the beeping of the beacon making it easier to find if you listen to it. The louder it is the closer you are.