Yes, it probably is one of those things we will never have access to change. SFC3's moddable UIs show it's possible, though.
Here are some sample problems with ships having too few hardpoints, excerpted from a readme I keep for my shiplist work (ongoing):
* K-B10 (and variants, including B11): the SFC UI does not have enough phaser hardpoints, nor are there the appropriate arcs available even if there were sufficient hardpoints. Therefore, I have followed Taldren's example in assigning the phaser type placement and arcs. Instead of 7 Ph1s, 8 Ph2s, and 6 Ph3s, the B10 has 9 Ph1s, 6 Ph2s, and 6 Ph3s. I've adjusted the phaser arcs on the B11K, but they are still inaccurate due to the restrictions of hardpoints and arc availability.
* Z-BB: Because there are not enough heavy weapon hardpoints to give the ship 2 FAL and 2 FAR disruptors, I?ve increased the arc on one set of 4 disruptors from FA to FX. This provides extra overlap, but I?ve left the BPV alone since the ship loses some Ph3 and Ph1 arc coverage due to the broken LWX arc and lack of proper side and forward arc combinations. The rear Ph3s and side Ph1s are now LS/RS.
* K-FWE: It needs more phaser hardpoints (7 different arcs) than are available on the F5/destroyer UI. To get enough hardpoints, I used the D5/war cruiser UI, but retained the F5 ship model. As an alternative, the F5 UI could be used if the FHL and FHR Ph2s were combined into one hardpoint with an FX arc (not KFX), though this would give the phasers more coverage than they should have.
There are others. I just didn't take notes on all of them.