There's a (in)famous software development quote, relayed with tongue firmly in cheek: "Hey! It compiles! Ship it!"
In software development, there are many steps a conscientious developer must go through between writing the code and sending ("shipping") the completed product to the end-user. A willingness on the part of the developer to ship as soon as the code compiles indicates either extreme hubris or carelessness: no testing has been performed by the developer (to verify that the changes work and haven't broken anything else), no 3rd-party testing has been performed (to verify that the change doesn't break other systems and is acceptable to users), no documentation has been written...
So when used by someone else in regard to your work, "Ship it!" implies confidence in your abilities: "You're one in a million, man — I have confidence that it'll work as you say it does."