I've gone through this thought process before myself but I didn't act on it.

Another idea...pull the two nipples out of the water pump housing, weld them shut at the bottom, re-install them and put the hoses back on.
It would work, but takes more time to go from functioning to closed as the nipples need to be swapped for functioning ones.

Another idea...If you can manage to tap and plug the ID of the nipples, from the top, then that would be much easier to work with.
This seems to almost be the idea you were speaking of?
I don't know if you'll find pipe plugs the proper size since the NPT dimension is the OD of the nipple, not the ID.

Maybe regular steel allen set screws could be used instead.
With some anti seize and or maybe teflon pipe dope, maybe they wouldn't get stuck.

Some quality time spent with a caliper and thread dimension chart will tell the tale.
There's not much material to work with inside those nipples so may have to go metric/finer increments to get a good fit.

It seems to me that if you tapped the ID of the nipples, and used regular straight thread fastener (not pipe), it might be
less likely to get stuck in there. The only issue I can think of is, the internal cutting/tapping will slightly weaken the fitting, so
you'd have to use your best judgement on that.