First of all, I don't think that the Bentusi have "completely alien" systems necessarily. Remember, you were able to send them resources, and more importantly, they were able to send technology - presumably as information to you in Homeworld and Cataclysm. That implies that they had some way of interfacing with you - either they really can reverse engineer alien computer systems quickly, or there is some sort of Galactic standard that the Kushan learned when they captured the Taiidan system. Whatever the case, it is clear that by the fact that they even can send technological plans and audio communications to you in a format that you can use is evidence that there is some sort of interface, and given that the plans were nearly instantly available, I'm presuming that they can send over executable programs.
In computer science, there is the notion of a Turing-complete language. Theoretically, any universal Turing-complete system - this includes Turing machines, computer programming languages, and quantum computers - can execute instructions that are equivalent to those that can be done on any of the others with sufficient programming and interpretation of data. To be of practical use (so they can add new ships and manage a bigger fleet), presumably the Kuun-Lan's computers would be such a universal system, and the Bentusi would be capable of sending over a program that can manage construction of ion fighters - even if the Somtaaw have no idea how it works.
Especially, since in the ship descriptions, the Super Acolyte is described as having a "crystalline energy source" that is "3 to 4 orders of magnitude" (traditionally, "order of magnitude" means power of 10, so that's 1000 to 10,000) more powerful than anything the Somtaaw have, and several ship characteristics are listed as unknown. It seems that the Bentusi simply sent over a "black box" in which the Somtaaw simply put in RUs and get out Super Acolytes - with the Somtaaw of having little idea of how the insides work.
Secondly, why is it so hard to believe that the Bentusi, when they were preparing the ion fighter plans/program to send over for the Somtaaw, that they added a few lines of code here and there that deleted the program after a certain trigger (say, destruction of Naggarok, or a signal from the Bentusi, or a time limit) was detected? It could even be passive - when the program was run, it'd make a check, and if the date was after a certain point, it would delete itself. If you've ever used shareware, you probably have had the experience of having those popups which say "You have 5 days to register!" or which say "Your 30 hours of use is up!". Really, there's no reason you couldn't have a program uninstall itself in a similiar manner. (And similiarly, the onboard computers on the ion fighters would be running when that trigger happens, and could lock up and command the fighter to retire to itself). If the Somtaaw never run it, though...well, then, they can't build any ion fighters anyway. And, remember, not only are the Somtaaw systems possibly alien to the Bentusi systems except for an interface, but it works in the reverse direction - such that the Somtaaw may have no idea how the Bentusi program works, except for the interface.
Or let me put it this way. Let's say that you had good reason that there was a time limit in your operating system that would cause it to self-destruct. So, just do us a favor and reverse engineer Windows (or whatever you are using) and scan it for any such code. Of course, in this scenario, the programmers didn't include any documentation on the code, since of course, they don't want you playing around in it. Oh, and you have maybe...24 hours to do it. Maybe 48. I don't think that's reasonable. You might as well be a Wright Brother trying to figure out a F-22 in a day or two before the technology is withdrawed.
As far as the siege cannon...well, the backstory does claim that the Kushan turned inwards sometime after Cataclysm. Also, the Somtaaw wanted to "bury the past", even retire the Core. I could see them retiring the siege cannon - which is primarly a heavy offensive weapon, useful for attacking huge ships like the Naggarok - of which, the only examples seem to be the Bentusi Tradeship, who are allies - and for thinning out fighter swarms - though it's probably safer just to use anti-fighter weapons. I get the impression that during this inward turn, most Hiigarans began to grew secure and the Imperials as a threat were reduced - because they were fleeing outwards where they'd meet up with the Vaygr. So, there really wouldn't be a need for the siege cannon. Or for that matter, given that Karan Sjet seems to have great influence and authority that everyone respects, she could have just told the Somtaaw to retire it, and they might have willingly complied because of her seemingly mystical knowledge provided by the Second Core.
Or failing that...maybe a Turanic or Imperial saboteur blew it up. They destroyed some of the modules on the Kuun-Lan before, maybe they could do it again...
Multi-ion-beam technology...The Somtaaw MBF had weak ion cannons. An ICF is better in terms of delivering power against a single target. But, it's quite possible that the MBF technology was adapted into (or contributed to) the pulsar beams on the corvettes and Battlecruiser. Or, it's possible that there were other ships more suited for the anti-strike craft role than the Somtaaw MBFs. After all, the missile volley of a few Missile Destroyers could pop whole wings of fighters out of the sky. (Whatever happened to that technology, anyway? I think its absence is just as strange than the Somtaaw MBF story-wise, even if it would be unbalancing...)
Finally, though I can understand what you mean with Homeworld being more realistic than Cataclysm... Um...just when exactly did hyperdrive (or FTL drives in general) become anything more than occasional speculation? Personally, I think a siege cannon is actually more realistic than FTL drives, which would have to invoke unknown physics, be suspectable to pesky quantum fluctuations that may destroy it, and according to current calculations, would need the mass-energy of like, a galaxy, as fuel to operate...
(Or for that matter, why exactly is the phased cannon array of HW2 more realistic than the siege cannon?)