You didn't specify if you are using c/c++ so I'll assume c++.
The easiest way to do this would be to pass around your VAO id. For every object that uses that mesh just have a copy of that VAO id. When you get ready to draw a missile for example you just bind the vao, send in your objects world matrix ( to the shader uniform ), and draw. This is called instancing.
Another way to handle it is more work but more robust, create a Manager Class that manages your Meshes. You have a vector of pointers to mesh objects ( use unique_ptr ) in the mesh manager and you can get a pointer to a managed mesh object, from that Manager class, by file name.
Managing Textures and Shaders can also be done in similar ways.