Hmm. I feel like this is assuming that "having weapons in all slots" is a good thing regardless of *why* there are weapons in all slots. I don't think that holds up - having weapons in all slots is good if you, well, want the weapons that are there and mean to use them.
Just having some random stuff there - or the cheapest possible, to be able to max out vents - or some other idea (say, not having weapons in a slot reduces armor, or w/e)... I think that'd just make a loadout feel messy, because you're putting weapons in for some reason other than actually wanting the weapons. "Put the weapons in a separate group and never fire them" could become a thing, etc.
I'm not entirely sold on the premise that "always have weapons in all slots" is good. If that were a goal, though, then I think the solution would probably involve increasing ship flux budgets (which could be troublesome to iron out balance-wise) and/or adding some very low-end, low-flux options for ... probably small and medium ballistic/energy slots. Though even if these cost 1-2 OP and generated no flux, it might be a hard sell in a lot of cases.
It seems like there is also some potential in somehow making burst damage potential "better" (which would make an over-fluxed loadout more desirable), but I haven't really thought that through, so that's mostly theoretical...
I 100% think it should be a viable option to "under mount" a ship, but I also feel like it shouldn't be the go to?
From a casual perspective "moar dakka" is intuitive and fun (just seeing your capital armed to the teeth is a nice feeling), but there's a heavy learning curve on kitting out some of the larger ships, making it very easy to accidentally over spec them.
I think the first thing to help with this would be clearer feedback on flux stats. It's SO important but it's just "more numbers" on a screen that's already overwhelming with them.
Having flux dissipation right next to(not on a line below) weapon flux (both on the main screen and the weapon group screen) would help really draw eyes on the idea that comparing these two numbers is super super vital. Bonus points if you can color code the dissipation number on some % scheme (super green when it's 2 to 1 and super red when it's 1 to 2 or something). Or maybe just put the % efficiency right next to it instead (numbers easier than colors? I dunno UI is the devil and its half my job).
This, again will help beginners really keep an eye on both the actual ships overall flux, and what it looks like for each weapon group, hopefully also teaching the idea of strategic weapon group usage/show off why missiles can be so good.
Somewhat related to this is the fact that ships don't come stock with weapons, unless recovered (and post salvage with a few). There are premade loadouts, but as a beginner i'd click on those, get annoyed that I didn't have all the weapons an it just "winged it", now had no idea if that was any good, and basically gave up with it (since hunting down a bunch of weapons just to test a maybe ok loadout isn't exactly fun with rng shops and no idea how to tell what planets might have what you're looking for).
I feel it might help if they did, and even if not, if maybe more premade loadouts were under gunned. Really drive home there's some great builds that center around putting on some killer weaponry but not bothering to fill out the rest.