before 0.95 i would have said that the HB generally is superior, as before it was the "general use gun" for a medium energy slot, for when you dont wanna think and just want to hold LMB, use it against shields and armor and hope that your high-tech flux superiority can make up for its inefficiency. but now that ive played 0.95 for a while i really dont see an argument for why the HB would be better over the MB, and thats because of the specific niche these weapons are in now.
energy weapons have been buffed to be more competitive, specifically regarding anti-shield. pulse lasers and ion pulsers are now without a doubt THE medium energy weapon of choice for anti-shield supression/flux building, whereas things like the PL, HB, MB (and amusingly enough even the HBPDL) are your choices for armor-stripping. and when you think about it in their role of anti-armor guns instead of generalists, the MB is superior. even if it has the flux ratio of the gauss cannon, it is 10 instead of 12 OP, and you shouldnt be thinking of 2 OP as "oh thats just 400 caps or 20 vents", but rather as something that can make or break a build, as the OP counts in starsector are so low that leaving weapon mounts open is common practice. these 2 op can be better PD, a reaper, or a hullmod that you can fit in, and as much as i would have preffered a "modular specializations" kind of deal, where hullmods are very cheap but have very strong specific debuffs, with the way it works here, in a game where you have an avg of around 120 or so op on a ship, of which some will be vents, caps, and hullmods, it would take more than just "better but still not good" flux efficiency to justify paying 12 over 10 op.
not to mention its armor cracking advantage is even better with short range EWM as Kanjejou pointed out, which is the playstyle youll be going for anyway with most ships that feature a med energy slot.
of course none of that is even tangentially important compared to the fact that MBs have that brilliant civilian-industrial charm, so i dont see how the heavy blaster was even supposed to compete against that