Right now the only way I can think of a shipping line shrinking is through very old ships being retired while there are other ships idling (or getting their ships blown up). I know in the changelogs Steve sort of shoots down the idea of explicitly modelling operating costs, but maybe that would be a good way to have civilian shipping more closely model the economic activity of the empire. The admin overhead just reduces the growth rate as the shipping line gets bigger and doesn't really do the same thing.
Also I am once again asking for mineral transport contracts (esp being able to peg it to reserve levels).