I'm not sure you noticed that you've basically answered your own questions there. "With ship upgrades they've discouraged building on planets, and it'd be contradictory to have said upgrade system in place when your ship can get blown up."
They intend to re-encourage building on planets, with farming, colonization, and who knows what else. To that end, ship combat could serve to make the ship less of a mobile home - upgrades would allow it to be better protected, to house more crew, more systems, more weapons. You would only be able to keep a whole town inside your ship if you never took it anywhere potentially dangerous, if you gave up on exploring.
FTL was mentioned way back when as a possible inspiration for ship combat, and I hope you remember that FTL's ship-to-ship combat, and indeed the whole ship structure, is basically room-based. Every room is a potential target point, every room can house one system. What do ship upgrades in Starbound do? Give your ship more rooms. More space for valid rooms, and bigger rooms. I'm not saying that it will happen this way, because really I can't know, none of us can, but I do maintain that it's a possibility - that ship upgrades could be setting up something like this, where you'd have to have valid enclosed (with airtight doors!) rooms like you currently have colonist housing, except you'd do this in order to put particular "furniture" there - weapons control, shields control, anything you might want to have crew manning or interacting with, each with particular requirements for size or shape.
Thinking in those terms, allowing players to just set up their ship willy-nilly opens too much of a balancing problem because there are bound to be all kinds of ways you could confuse or trick the AI - not to mention that lacking Terraria's block variations, most player-created ships are just going to be bland to look at compared to mostly hand-drawn designs.
I'd be mostly fine, by the way, if there was a special ship builder you could use. Like, "here's a something-by-something background object, you have to place it and fully enclose it to have it count as a room", limiting the player's freedom in regards to how many discrete chunks the ship can be split into, and the size and shape of those chunks. Like when you remove the default backwall paneling in the ship you can see the windows and some kind of machinery behind it - that's what I mean. So that you can't just backwall a section of empty space and call it a room.
Final thought: Currently you are never sold a "ship upgrade". You are merely sold a license. Seeing as you can never die in the game, it would entirely make sense if you could never lose your ship either - you just have it rebuilt thanks to having a license (and S.A.I.L. backups), with some hefty fee, and whatever mechanic is chosen to determine how much of the stuff you had there is preserved. Maybe your furniture and decorations are recreated but any container contents are lost, that sort of thing, unless you go back to where you were destroyed and pick through your last ship's debris for anything salvageable.