Cryton, I think part of the problem between your view and mine is the definition of "small ship". When I look at the 5,000 dTon limitation for ships, I see 25,000 Gross Register Tons of ship space or 67,500 to 70,000 Displacement tons of ship mass, and mentally think, that is not a "small ship". The following are some of the ships I use as examples.
WW2 Liberty Ship: 7,100 GRT, equal to 1420 Traveller dTons
WW2 T2SE Tanker: 10,200 GRT with a capacity of 141,000 barrels of petroleum products, equal to 2040 Traveller dTons
WW2 FS Freighter (Army cargo ship used mainly for inter-island duties): 560 GRT, a mere 112 Traveller dTons
Great Eastern (Built in 1854-58): about 18,915 GRT, or 3783 Traveller dTons
Edmund Fitzgerald (Great Lakes Bulk Carrier): 13,632 GRT, equal to 2726 Traveller dTons
RMS Lusitania (sunk in 1915): 31,550 GRT, or 6310 Traveller dTons, a bit larger than the 5,000 dTon limit
MV Paul R. Tregurtha (currently the largest ship operating on the Great Lakes); 36,360 GRT, or equal to 7272 Traveller dTons, about 50% larger than the 5,000 dTon Limit. The Tregurtha is over 1,000 feet long with a beam of 105 feet. Seen up close, the ship is staggering.
The new RCCL Harmony of the Seas cruise ship is 226,963 GRT, or 45, 393 Traveller dTons, so much larger than a "small ship" universe, but not that big in a "large ship universe" of one-half million dTon dreadnoughts.
If I think in terms of displacement tons, then the limit of between 67,500 and 70,000 displacement tons includes the RMS Lusitania, the RMS Titanic, the Iowa-class battleships, Midway-class aircraft carriers, and just misses the Paul R. Tregurtha, if fully loaded with 68,000 tons of taconite pellets.
My "small ship" universe does not really have small ships. For an example of what a Liberty ship could carry, see the following site.
http://www.usmm.org/capacity.html
As for building yards, I would rate a yard capable of only 5,000 dTons in 36 months as a very small one. Assuming misjumps occur and accidents happen, I would assume a loss rate of about 2% per year of commercial ships in operation. The 1977 rules have a misjump on a role of 12+ every time a ship jumps, or a 2.777% chance, so the more times a ship jumps in a year, the greater the chance for a misjump. Based on that, the 2% a year loss rate is quite conservative. You also have to allow for yards doing routine maintenance or required overhauls.
It should be noted that I am looking at the building rules from the stand point of nautical architecture.
As for the military overhead, the logistic overhead required by an Imperium-wide force will make for a very large number of support personnel.