Plus, what's most important, in neither game, it really matters that the world is 3D. Starships can go just anywhere, you see something on the 2D map, click, and they go there and start shooting. It's actually closer to 1D (move forward, shoot) than to 3D.
For a single action with only a starting point and destination, yeah, the action is rather flat. But when you have multiple objects and multiple possible destinations, the relations between all of those elements makes the 3D relevant. In a mission where you have your blob of ships and the enemy has their blob of ships, the relations are rather simple. As soon as your enemy has multiple blobs of ships in different locations, and/or there are resources in multiple locations to harvest and defend, you have to start making choices which inherently involve cubic space rather than square space.
I can't recall feeling that the campaign missions did a very good job of exploiting that third degree of freedom for maximum intrigue, but the mechanics allow it. Or maybe I simply didn't have enough cleverness to see advanced tactical options that the 3D offered, always just taking the direct approach when I'd have been more effective with creative flanking maneuvers, splitting my forces, splitting my enemy's forces, and so forth.
For me, a truly 3D game would need to have mechanics where it really matters that you are in a 3D world. Yes, there are "cliff like" elements in a lot of games (like unit on roof in X-COM), but that is really just 2D with a barrier and with "portals" in between (ladders, ramps,...). Other than blocking other units, it does not really matter.
True, there are ways in which alleged 3D space is barely more than complicated 2D space with walls and portals. But there are definitely cases in X-COM where it's more than that, especially since units are able to hover in air. For example, if I'm walking down a 1-tile alley between two buildings, in a 2D game I could only have 1 unit in front with full line of sight, and all the other units behind with blocked sight. In X-COM, with the right technology, I can hover one guy over another and both of them will have full line of sight; or three or four guys. If the alley is short and I'm at the back end, I can move my entire stack of soldiers one tile to the side to take cover behind the building, and later have them pop out of cover again together.
There are all sorts of tactical scenarios that can be created in X-COM's 3D environment that can't really be replicated in a 2D game, such as Jagged Alliance (even the JA2, which had the severely limited kind of 3D which you described). But as above, if a player is flexible enough to recognize and exploit the 3D space to its fullest is another question.
When you shoot downhill, you suddenly have twice the range. When you march uphill, your units' stamina is depleted, and they are easier to hit. That is true 3D.
Personally, I'd prefer to emphasize that this would be heterogeneous 3D. The third dimension is real and relevant, but it is different in quality than the other two dimensions. In Homeworld, aside from the user interface treating up as special, all three dimensions are identical in nature, which might contribute to the feeling that the third dimension doesn't add much of value over 2D. Nonetheless, when four or more objects are in play, there are still spatial relationships that can exist in Homeworld that are impossible in a 2D game.
In X-COM it's a little trickier to classify because for units/objects that can freely hover, the three dimensions are homogeneous. But for things that are affected by gravity (units without hoverpacks, objects like grenades), the vertical dimension is distinct in nature from the other two. But that's kinda cool because now you need to simultaneously think about two different kinds of spaces which overlap: full 3D space and gravity-bound space. And your adaptation to those two overlapping spaces will depend on which units and equipment you have, your opponent has, and civilians have. The combinations lead to an enormous variety of tactical circumstances, and thus a lot of interesting gameplay.
