Yes, but if just starting construction on, or even researching, a WMD causes everyone to become hostile you may never get a chance to implement it.
Sounds like fun, really. Why even waste development time on implementing this if you obviously don't want it to be used? But see below, the root of the problem is a different one...
Some examples would be a Wonder in AOE, or the TEC cannon in Sins, possibly the space ship modules in Civilization, your super-weapons in C&C.
I think I see where the problem stems from.
This isn't to be a 4X game. It's an elite clone / space shooter with added RTS elements to make fleet management feasible, as opposed to the messy excuse of an interface the X series had to offer. And to be honest, I'm not even sure if Josh should implement research, as I see little gain for a lot of extra effort, but instead several cans of worms being opened, among them balancing and reducing the need for exploration in the first place.
In those 4X games you mention, the stuff you describe are game-enders. Once they're built, you either win, or are pretty close to winning. In a sandbox space exploration/trading game, these "win conditions" don't exist, as such the "super weapons" can't be game enders. Instead, they're what it says on the tin - weapons, with a large possibility of making the game unfun or the challenges trivial (depends on which side of the barrel you end up, really).
And now let's ask ourselves again: Why would we want/need those? What would they add to the game, how would they make it more "fun"?
Because, at the end of the day, this is what games should be about: fun. Not the implementation of features that make little to no sense either "because you can" or "because game X had it".
Also remember that this is a one-man show. Resources and time are limited, and while the budget has shaped up rather nicely in comparison to what was planned, Josh is still operating on a shoe-string budget compared to a large commercial production. As such, he shouldn't waste time of stuff that's a hassle to implement and adds little to nothing to the game experience.