Hi and welcome to the forum!
Not too long ago we've kind of made a tolerance regarding the modification of ship's textures. There is a new board created for this: http://forum.shipsim.com/index.php/board,124.0.html
In a nutshell, you are allowed to repaint various ships in SSE. The only condition is that if you post your modification here on the forum, it must remain true to the authenticity of any real vessel. This because Vstep is in contract with a number of ship owners who have their ship placed ingame and do not want to see their ships painted pink with skulls and flames on it. For fictional ships this is of course less of an issue as long as you keep it decent.
For private use, go as you please but remember that technical support is seized when you start altering content unless you make a clean reinstall of your game.