Not just missiles fail in my game. Lasers too must be aimed on head or fail. It's a shame, because i remember to shot legs all the time in this game. It worked without miracles, if a leg was there, you can shot it. Now its almost impossible. Seens to be some Dosbox problem or something. In original game i never empty my laser on just one enemy leg. Clearly buggy to me. If i got time, I'll install Windows98 and sci-tech display doctor to VESA drivers and see what happens. But this coult take months to happen.
Some enemies are impossible to shot on legs or body(the stick legged and chicken-lizrds ones) thus, making then almost invincible opponents. When i an out of missiles to shot in ground, and laser to shot seeking "secret" shootable parts at distance, my missions fail. I must hope the mission got some missiles in ground, because primary weapon isn't working. And missiles only work with a workaroung(nice tactic, but still the only option).
I need help. I'm using an Athlonx4 2600MHz with 4gb memory DDR2-800MHz and Radeon 4670(yeah, i really like this game like this, to use it there).

It doesn't need to be a dosbox problem, although updating to
0.74 is always a good idea.
it might be problem specificly to the game version used by GOG.
So maybe try that on a normal pc or use the version that works with DOSBox.

I did some testing and it may be due to frame rate issues like Interstate 76.
Installed the game on MS Virtual PC running Windows 98. It ran ridiculously fast, and every shot went straight through the target without registering.
Next, tried GoG version, but reduced the CPU cycles in DOSBox down to 25%. Nearly every shot hit, but the game was a bit choppy.
So it may be possible to find a setting that gives a good compromise between frame rate and hit detection.