Perhaps a compromise? We could have shipyards, and there are different ways they could be used. By putting blocks into them, it would build ships for the cost of the blocks and be faster than method 2. Method 2 is that you use credits and it builds the blueprint at ~75% speed with about a 25% price increase. That way, using blocks is more effective, but credits are still a universal currency, as they should be. Of course, the economy would need to be overhauled for this, and the percentages would be configurable, as well as the option to disable block construction, credit construction, or both for a non-bluepront server.
Could work, I suppose, but even though it would reduce the issue, the core mechanic allowing for blocks to be created out of nowhere would remain. I do believe this is something the game needs to rid itself of entirely, not just make a bit less practical.
I want "3D printer" style shipyards; where you provide the raw materials (e.g. ores and not blocks, because there's too many different types of blocks to fit them all in an inventory at the same time). If attached to a station with a shop; any materials you didn't provide would be auto-purchased from the shop by the shipyard.
Different shipyards would be different sizes, the same as the current docking/docking module system. Actually; it could just be a docking area, some astro-techno-beamo turrets, and a "shipyard computer" to control the astro-techno-beamo turrets and some storage.
A medium sized shipyard wouldn't be able to build a huge ship (and can only build ships that fit). A huge shipyard would do more "blocks per second" than a small shipyard; and consume more power.
The trading guild's shops would have medium sized shipyards (mostly for newer players that don't have many resources yet). Players would have to build larger shipyards if they want something that can handle larger ships.
When being built by a shipyard, the ship can't be removed from the shipyard (no undock until completion) and would be vulnerable to enemy fire (excluding protected sectors and faction home bases). When the ship is finished the shipyard would set ship's faction module before allowing it to be undocked, so that people don't camp shipyards and steal people's ships.
The shipyard would also give you the ability to de-construct a ship, repair a damaged ship back to what the blueprint says it should be, and transform a ship from one blueprint to another.
That's pretty much what I would want as well, especially the part about shops having small-built in shipyards, allowing the current blueprint system to continue existing in a much more balanced way. I have personally imagined that particular part not as shops having actual shipyards, but rather projecting construction beams of sorts from their rings. These would not have a size limit for the ship they build, but be way slow to build anything big in a reasonable amount of time. They would draw materials from the shop's stock, and require payment equal to, say, 110% of the total block price. For further awesomeness, I'd like to see such beams do other things as well, such as tear apart pirates or repair trading guild ships in the vicinity.
Also, why should shipyards use ores? Just let them draw materials from linked storage blocks and the inventory problem is solved.
And before anyone tries to say otherwise, no, block-by-block shipyards would not induce mentionable lag.