Just because you never encountered troopers manning defensive emplacements doesn't mean the Sith wouldn't use them. The game mechanics of KotOR prohibit many things, such as taking cover in a firefight, but that doesn't mean that it wouldn't have happened "historically". We know that the Sith had ready access to repeating blasters, and would make good use of them when planning their deployment.
But anyway, concerning these 'mounted assault cannons' - your basing this on the assumption that Traya's forces have this at their disposal. And it is highly likely that they do not, not only have I never come across manned turrets in KOTOR I or 2 but in the Battle of Telos IV the Sith invasion force deploys automated turrets across Citadel Station, it is said as much during the conflict. So this is likely what will be deployed. HKs are unshielded? Possibly but G0-T0 could upgrade them with standard personal energy shields, if they don't have these already which they likely will. But yes, ion weapons would be effective. But just as effective as the advanced weaponry of G0-T0's forces will be against the Sith and the assassins.
Are you belittling the skills of footsoldiers? Most of the "footsoldiers" I've known have been skilled infantrymen, and infantry excel at defensive warfare more so than any other type of troops. Furthermore, most of the troops stationed in the Trayus Academy are Sith Commandos, who would be extensively trained in addition to being seasoned combat veterans. They are described as such by Wookiepedia:
Let's also not overestimate the capabilities of these commandos, for in the end they are footsoldiers.
So the Sith forces at the Trayus Academy represent a well-armed and effective unit. They have disruptors, ion weapons, and repeating blasters, in addition to personal energy shields and melee weapons. They will easily carve up any assaulting force that tries to breach the Academy.
"Sith troopers were the primary infantry units for the Sith Triumvirate during the Dark Wars. [...] average Sith troopers were armed with Sith Assault Gun and Sith sniper rifle for ranged combat and well as standard stun batons and vibroblades for close quarters combat. All types of Sith troopers were issued with vibroblades for close quarters combat and may have been issued with Sith energy shields as well. [...] The weak would be siphoned out through the merciless Sith training schemes, resulting in an efficient and powerful fighting force."
"Sith commandos were elite Sith soldiers [...] They usually wore scarlet red armor and were issued light repeating blasters."
"Commandos seen at the Battle of Telos IV during the First Jedi Purge wore silver-colored armor. During the purge, the Sith Triumvirate deployed commandos on Dxun, Onderon, Citadel Station in orbit above Telos IV, the Ravager, and at the Trayus Academy on Malachor V."
"Sith elite gunners wore copper-colored battle suits. They were often armed with disruptor rifles, which were capable of penetrating personal deflector shields."
"Sith grenadiers were known to use grenades, mostly fragmentation or concussion types. They also wielded blaster pistols. They were also known to use thermal detonators in battle."
The Trayus Academy survived, it was just moved partially underground by the disruptions of Malachor V.
It seems perfectly plausible to me that the MSG is underground, else it would be effectively useless as once its activated the planet will be bombarded with debris and any structures overground will be destroyed. Including the MSG which will then be deactivated and the mass shadows will stop.
The Mass Shadow Generator isn't still causing the effects on Malachor, either. It was a one time event, used to manipulate the gravitational anomalies present in the system, causing tremendous damage to the area around the planet it was activated on. It could very well have been located on or near the surface of the planet, since otherwise it would be impossible to interface with it. The fact of the matter is that if it can be accessed by G0-T0's forces, then there must also be a way for Traya to access it, even if it is to only demolish it with explosives and prepare a trap for G0-T0's droids when they come to activate it.
Really, the only basis for assuming that the MSG is inaccessible is because we didn't see it physically appear in KotOR II. However, this is a very thin assumption because the entire segment with the Remote and G0-T0 on the planet barely made it into the game. For all we know, the interactions with the ship's drive cores was only part of the process originally intended to activate the MSG. Since at least part of Remote's activities on Malachor V happened "off-screen", perhaps he first visited the MSG and primed it before setting off to power up the reactors needed to operate it.