Traya is blind. She cannot sense the droids with the Force. A HK-50 assassination will work.
Note that HK-47's and T3's fates were unknown to Traya, she could not sense their future. Which means she will not be able to foresee a HK-50 attack. Nor will she be able to sense their presense, and they're assassin droids. They won't be giving anything away with sound, etc. She can't see them. She's blind in more ways than one.
Also, pre-cog "spidey-sense" works seconds before danger, not as it is approaching. So even if she force-cloaked, she'd already have blaster bolts flying at her from HKs she didn't even know were there.
Traya had expressed a disdain for droids on several occasions to the Jedi Exile. I don't think she will be taking GOTO seriously enough in this encounter.
(Unless she is unaware that he is a droid... the Kaggath only states that they are aware of each other, not that they know each other's secrets. GOTO was quite protective of his actual identity, masquerading as a human Exchange member)
Traya's underestimation of droids, coupled with her inability to see would certainly make her vulnerable to assassination by HK-50 Units, but not necessarily easy prey. Remember, she is still surrounded by Sith Assassins in her Academy on Malachor V, and so reaching her would be difficult without raising an alarm. It's more likely that the HK-50 units would kill her sometime during the war, while she was on the move and had fewer layers of security for them to penetrate.
The other variable to consider is whether GOTO can reactivate the Mass Shadow Generator on his own. It seemed that it was only with Bao-Dur's programming that the remote was able to prepare the weapon to be fired again. It might require significant efforts to trigger the MSG, both in the research phase and the physical arming of the weapon. This could alert Darth Traya that something was afoot and give her time to evacuate her stronghold on Malachor V.
Now, what are GOTO's vulnerabilities? His yacht is an easy target if decloaked, and he himself possesses very little in the way of combat abilities. His reliance on droids can backfire if those droids are reprogrammed or sabotaged, and due to his obsession with holograms and inability to meet anyone in person, it could be possible to spread misinformation among his allies and minions by transmitting false messages from him or otherwise impersonating GOTO (or a droid acting under his orders, as we see with T3M4 infiltrating the warehouse on Nar Shadaa).
The question is, what would the best opening moves be for each side?