Answer to original question is kinda complicated and has no simple answer, except that shorter barrels are "handier" and easier to fit into small spaces, such as vehicles. But in that instance, folding stocks are a better answer.
Yes, some folks have "chopped" their Mini barrels and have obtained better accuracy.
I kinda question this, since many folks, by chopping their barrels "may" have eliminated damaged muzzles. A simple and DIY re-crowning of damaged muzzles "might" have been far less expensive. Who knows?
Also, we now have decent "Barrel-Struts" for Pencil-Barrels which work very well in increasing accuracy with such Early barrels. Dual-clamp Barrel Struts FAR more effective than Single-Strut units, as per Mfr. Maybe not so much on any later "Heavy Barrel" Mini.
Latest iterations of Minis have more "meat" on their barrels than earlier versions and are more accurate, overall.
Longer barrels deliver more energy behind the bullet, thus increasing range.
With respect to common M-193 55Gn bullets, the bullet velocity when impacting soft tissue makes ALL the difference between bullet yawing/fragmenting within the target and simply punching .223 holes.
All this is aside from other more fundamental factors, such as the all-important fit of the barreled action to the stock. Most often this can be significantly improved for almost any Mini.
To directly answer OP's question, I think I'd take the longer barrel. At least you have options then.