Yes barrel length does affect energy but what energy remains is still quite large. The following gives ballistic for calibers. Note that a 45 ACP which is considered having good stopping power, its muzzle energy is for a 230 GR bullet @900 fps 440 FT/lb, Note this was a quick calculation so it might be off a little.
44 MAG Using the test barrel and the same ammo for each test. Link below
12 inch: 1541 fps 1100 FT/lb
8 inch: 1433 fps 975 FT/lb
4 inch: 1150 fps 704 FT/lb
3 inch: 1015 fps 485 FT/lb
A 3 inch might be a little less than half the power as a 12 inch 44 mag but the 3 inch is still above the 45ACP.’
The big advantage of the 44 mag is that you can shoot specials which can still meet ACP levels and if you miss you can scare the you know what out of the bad guy with the flash and noise.