With regards to the various healing (Senzu beans, Frieza's pod, wished back with the Dragon Balls), in order for that to correct any sort of mental injury, we really have to define what brain damage is in this context, and what those items do.
I assume the jump-off point for the theory would be the hit on the head as a child that forced his personality to do a 180. In order to fully discuss the matter, I'd need to understand what other evidence they're bringing to bear (battle injuries, modifications to personality, notable quirks, etc.).
We can assume that the various healing technologies are set in place to accelerate the body's natural healing processes. This may include any physical damage to the mind, but it will still be executed to the specifications and best ability of the body involved, so if something managed to get hooked up wrong before, that's how it'll stay.
I agree with you that the heart virus isn't an excellent example of the Senzu beans' limits in this regard; perhaps the virus is undetectable or otherwise protected from the host immune system. If we assume that the Senzu beans must work within the capabilities of the body, or at very least they can only amplify a limited set of processes, then it's plausible that the immune system would be brought to peak efficiency and any current heart damage healed, but the virus itself would not be eliminated.
A better example of the Senzu's limitations would be Yamcha. He's had several over the course of the series. One in the Android saga healed a hole through his chest without so much as a scratch left behind. And yet his facial scar has never vanished. His body doesn't seem to see this as damage, and so the Senzu beans are seemingly powerless to affect it.
If Goku has similar brain "scarring" of any sort, perhaps from very early in his life, it would stand to reason this wouldn't be corrected either.
Any logic applied to Senzu beans can be applied to Frieza's pod as well, which for all intents and purposes seems to operate on the same principles at a slower rate.
The Dragon Balls are a great deal more difficult to explain, but that's because things like the DB afterlife and the concept of reviving people whose bodies are completely destroyed, or how people can train in the afterlife and have those physical abilities carry over to the new body, or any rules or exceptions for the above, are all difficult to explain. They were never really intended to be looked at that closely. Again, it all seems to at least operate on the principle of bringing people back the way they were, so it would be unlikely to alter any of the chemistry or connections in the brain as a result.
What I would say is that there's no evidence that Goku's brain is currently malfunctioning - at least as a physical processor - but I could buy that he has some kind of mental disorders or deficiencies stemming from how it's wired up. And it's possible those could have been the result of brain trauma at an early age which has since healed sufficiently that the body has basically accepted it.
Further extrapolation is a great big crapshoot, but it's at least plausible. But without brain scans, or word of Toriyama, there's really no way to tell.
As to why any characters in the series wouldn't have commented on it, since he's functional enough that any aftereffects of the damage would be seen as personality traits or deficiencies, but brain damage doesn't necessarily cause personality traits or deficiencies, it's equally plausible that it could just be the way he's grown up and wired himself and, in the absence of additional evidence or necessity, people give him the benefit of the doubt. This leaves the question equally open, if irrelevant.