Even with the significant global mass reduction that ships appear to have suffered, it's hard to see how modules could come in at under 100 kilotons - that's only about as much as a modern-day aircraft carrier or cruise ship.
Well, if you assume that conservation of mass applies in GCIII and that the mass listed for a ship includes the mass of its cargo, then you can estimate the mass of a module by checking the mass of a construction ship. Of course, this has some issues, as the listed mass of a ship appears to depend only on its hull size (e.g. Tiny) rather than on what it carries, and moreover the masses seem to have been chosen more or less randomly; the default Terran bomber has an average density of almost 2.5 million kg per cubic meter while the TAS Crusader from the campaign has an average density of only ~20 kg per cubic meter (which, if the TAS Crusader is made of the same kinds of materials that the standard bomber is and the standard bomber contains no empty space at all, indicates that the TAS Crusader is 99.9992% empty space; densities are computed by volume enclosed within the bounding box whose dimensions are the length, width, and height of the ship, and while this does mean that the average densities could be much higher than indicated, the bomber and the TAS Crusader don't appear to differ enough from the bounding box to change the average density by more than an order of magnitude or so, which isn't all that significant when the densities based on bounding dimensions differ by about five orders of magnitude).
You could alternatively estimate how much mass a construction module could possibly contain based on the volume of the ship carrying it and some average density, but as noted above, the average ship densities in GCIII (and probably also GCII) are a bit variable, and of course then there's scaling issues even before you start playing around with component scale - if you fit a construction module onto the blank small hull and build it, and then do the same with a blank tiny hull, you'll discover that your two construction modules differ in volume by a factor of about 33; the bounding dimensions of a default-scale construction module on the blank Tiny hull are 4m x 3m x 7m (84 cubic meters) while the bounding dimensions of a default-scale construction module on the blank Small hull are 12m x 10m x 23m (2760 cubic meters), using the Terran ship set. I don't know what the bounding dimensions are for default-scale construction modules on the blank hulls for the other size categories, but I imagine you'll run into even more issues determining how big a construction module is if you were to check against those. Internal consistency isn't exactly GalCiv's strongest point.
(Actually, it's not entirely true that the masses appear to be random. Taking the mass of a Tiny hull to be 1, a Small hull has a mass of 2, a medium hull has a mass of 3, a large hull has a mass of 4, and a Huge hull has a mass of 10, while Cargo hulls have a mass of 3.6. According to the game, Tiny hulls have a mass of 73500 metric tons, roughly on par with a real-world aircraft carrier despite typically being smaller than real-world fighter aircraft; GCIII small hulls have a listed mass of 147000 metric tons, or roughly two aircraft carriers, despite being only a bit larger than a real-world jet fighter. It would perhaps be more fair to say it looks like someone picked what they regarded as a nice progression of mass without really thinking about what it meant.)
Besides, a fully-upgraded star base in GC3 is, what, 90-odd modules
I asked the computer to count this time; there are 43 generic, 25 military, 21 economic, 10 mining, and 7 culture modules. A fully-upgraded starbase therefore runs from 50 to 68 modules if there's at least one precursor relic in range to enable the archeology stuff, or 45 to 63 modules if there is not.
that's 9.75 million tons there and then using the (imo conservative) 0.1 per module measure.
One thing worth noting before running with the old GCII mass metric is that in GCII, you kept the old module when the new one was added to the station. In GCIII, the new module replaces the old (or so it would seem, since the old module's bonuses are lost, though where the pieces go is anyone's guess, and we already know from the behavior of ship components that there's nothing specifically preventing the old weapon, sensor, and defense components from stacking with the new; the behavior of planet improvements such as factories and labs suggests that the starbase factories and similar are refitted when the station is upgraded with the new version of this), which would suggest that a GCIII station's mass would be more or less constant except when an entirely new module line is installed. It does beg the question of why the newer modules cannot be installed directly, skipping the older versions, but then that's also true of the planetary improvements.
I know some people are against having so much power on MSB to defend planets, so maybe MSB should have some modules that give them production and a shipyard so that you can still function if all your planets are taken. I know this idea is terrible as where would the economics come from for fleet maintenance but honestly I don't see why someone with 50 MSB and large fleets defending them should lose the game if they lose all their planets to transports going around the MSB. They'd still have an amazing faction power and should have the chance to come back.
While I can see an argument for not wiping out a faction until it loses the ability to take a planet, I'm not terribly fond of the idea of allowing starbases of any kind to sponsor shipyards.
As far as defending planets goes, I would be okay with military starbases being capable of supporting a small garrison force or some such thing on nearby worlds, though it would need to be done in such a way that the garrison actually takes time to be replaced rather than coming back for free every time a battle occurs (or, for that matter, each turn, unless it's a really cheap garrison force). However, I would not be okay with these garrisons being fleet replacements to any significant degree. Prevent the loss of a planet to an attack by an unarmed and unescorted transport or group thereof? Sure. Prevent the loss of a planet to any real commitment of force, though? No.