Should there be a direct counter super weapons ?

Is it good game design to include a unit/structure that with minimal micro completely shuts down; nuke, drp, zenith and starlight.
In the same way that that ulti counters fat units.

No

[Spoiler]

I find it interesting if there are conditions under which superweapons fail to win:

- Fail to provide enough AA and get bombed
- Fail to control territory in tac range of your super or to have a bunch of Funnelwebs guarding it -> get tacnuked
- Fail to provide a flea screen -> get ulti'd
- Fail to have enough antis -> get nuked

I don't think there needs to be anything on which you can rely to beat a superweapon though.

Properly built porc can beat off an astonishing amount of attackers. It's probably a good thing to have a superweapon or a game could last for hours even after a team is doomed.

That said, there are a few counters.

1) Silo. Mass launched shockleys can incapacitate a SW for long enough that a team can win
2) Massive air bombardment. Often guys build a SW without proper air defences. I've seen airstrikes kill a DRP more than once.
3) Another SW. You can always build your own.
4) Nux. A SW with insufficient antis can be beaten like that, in the sense that a nuclear strike can soften up the defences enough for attackers to get through.

Usually a SW happens when one team has massive eco superiority and the other doesnt.