Very easy to fix (from a human player stand point, not sure about the ai), have a surcharge on either individual components, or components thresholds.
So keeping existing costings, and add:
1. A 1 component ship adds +1 to cost, two competent ship +2 to cost etc, etc
2. Ship over 300 components have a + X amount cost, ships over 500 components have a + 2X amount cost.
The above it just and example, the rate, scaling and so forth could be easily tweaked for balance, but the end result should mean one large ship will be much more expensive to build and maintain then five smaller ones (with the exact same components, just spread out more).
Edit: Thought a bit more about this, and IMHO it should be a law similar to diminishing returns, where the costs go up exponentially. Aimed at VERY large ships being a special commodity, (ie a large civilization might be able to afford 3-4 of these things, and the loss of which should be a major catastrophe. (Admittedly I am coming from a star trek stand point, where ships take a few years to build, not coming of the production line like hot cakes-a separate issue that I have modded for in my own games)
< Message edited by zoommooz11 -- 10/13/2014 1:02:27 PM >