I believe supersonic loads out of handguns are in general less accurate than sub-sonic loads. But not in and of themselves, but due to human factors. Generally speaking.
The physiological response to supersonic shock waves hit the face and brain, causing a small amount of trauma, and sometimes a little bit of pain. You can train enough to overcome this, and I had at one point.....but I like leaving my indoor range without a headache if at all possible. It's similar to blink when an object approaches your eye...it just happens. Flinching happens involuntarily when things start happening to your body that it doesn't like.
I choose "heavy for caliber" rounds if possible if I'm nearing the supersonic threshold, to keep them beneath if I can. If you have loads that are "right on the line" a good example is 180gr 40 S&W or 147gr 9mms with extreme spread, some go above and some go below, and you can easily see and feel the difference even out of the same magazine.
Swaged pure soft lead going around 700fps with a fast burning powder is a thing of beauty out of a .38 but hard cast alloyed bullets going that slow, with lower pressures won't perform as well, generally speaking. They are better for me at 900-1100fps with higher pressures giving the harder bullet that requires more pressure to push through the rifling, and a tad slower powder works better.
Jacketed bullets also like to be pushed a little harder, due to more resistance.
Some of the least accurate loads ive ever fired were jacketed bullets with a very light mouse-fart charge in .38 special.
I may be a bit off on my understanding of the science, but I know enough to know there is a difference and I react accordingly, and it works well for me. Obviously others have different experiences, and I fully understand that as well.
