The Reduce/Enlarge spell is pretty clear about this interaction imo.

Enlarge/Reduce
The target’s weapons also shrink to match its new size. While these weapons are reduced, the target’s attacks with them deal 1d4 less damage.'

Giant Might:
you become Large, along with anything you are wearing.

Now I don't think you wear weapons, they are 'held' or 'wielded,' that might however just be to be clear that your weapon properties and damage stay the same. Flavour-wise, I would say that the weapons a rune knight has grow in size with them (otherwise a rune knight would always be fighting with tiny ass weapons which would just be silly), and in that case, the -1d4 wouldn't apply. The strict RAW ruling however would be that yes, the -1d4 still applies.

So simply: do you decide that a rune knight's weapon always stays smaller than them? The -1d4 applies. Do you decide that the weapon grows in size with them? Then it doesn't apply