Small ships and one to a few BIG ships: dispersed structures with affordances to carry freight, smaller ships, some manufacturing capability, labs, and habitat modules.
- Drop off a "trading post" and some cargo shuttles, pick it up when the trade opportunities diminish.
- Position and replenish deep space waypoints to enable advantageous trade routes.
- Actual offices in orbitals and on dirtside for important worlds.
Depending on 'culture', you might have a "homeworld", or some arbitrary place for a regular (biannual? decadal? every generation?) family reunion/shareholder meeting.