There were a few issues that led us away from letting people build their own weapons block by block. We agreed that it was definitely an intriguing idea, but some of the issues included the need for a new micro-block system, which would mean the game would be calculating even more individual blocks to render as more and more players entered the same area. Determining weapon output location, and how the weapon would be held, and how that would interact with the player model was another big issue.
Something else to consider is that we do obviously love focusing the game around building, however another aspect of the game hasn't been pushed a lot in the past, which is exploration. By using a modular system for weapons you are encouraged to go out into space and hunt for parts that will make your weapons stronger, faster, more efficient, etc. This system also aligns with our plan for fauna, going with a modular approach which will allow the game to create interesting combinations for the player, thus filling the universe with more interesting and diverse weapons, just as we'll have varied fauna, while keeping it very controllable from a back-end standpoint.
StarMade is all about freedom to the player, to play, build, and explore how they want. We understand that not using a block-by-block building mechanism removes some of that creative freedom, however we have to consider how such a system would be handled not only by the game, but by the players and their computers. Hopefully this gives some insight into the reason for the direction we're going. I'm personally very excited about it, as we (currently) aren't just planning "boring" modules like stocks, barrels, etc. but modules that may drastically change what, and how your weapon fires. Again this is all still very work in progress, so don't take any of this set in stone. That's just the current plan. Let me know if you have any further questions.