In second mision there is pirate ship and there is box inside ship room. When is opened there is number (0417) and when I get a loot, it change to 0418). I don't know what it means, I tried add this code into machine which open doors, but it nothing happens.

Does someone know what this code means?

I played this game very long ago, and I can't remember if it usable or not.

I think it's just some worldbuilding. The pirates had a safe box with a counter for how many times it has been opened (or something like that). I'll leave it to you to work out why.

According to https://www.ttlg.com/forums/showthread.php?t=41869&=460595&viewfull=1#post460595 it increments when a spice bag is picked up. Why it exists, nobody seems to know.