Shipyards have at least a computer terminal where you can repair any damage to your ship or buy and sell expendables like missiles and torpedos or various upgrades, like better weapons. You sell parts generally for half the price you bought them for. This means buying e.g. a Gun Boost Mk II, only to replace it with a Mk III later means losing half of what the Mk II had cost.
All but the smallest shipyards also offer a small selection of new ships for sale. Just walk against one of them to make the ship dealer talk about it. They are not cheap, but the starting Tarsus, though versatile, is so inadequate that one should switch to a better model as soon as the finances allow it.
The Galaxy is arguably the most direct upgrade to the Tarsus in all aspects: it is faster, stronger and has a larger cargo hold. And it is just as versatile, suitable for both Merchants and Mercenaries Guild missions, though not the optimum choice for either. If you're only interested in fighting and Mercenaries missions and don't trade then an Orion and much, much later a Pegasus would be best. On the other hand if you prefer trading and Merchants missions and avoid fights then a Ulysses and eventually a Drayman may be right.
A new ship comes without any extras at all, not even a Jump Drive. Calculate accordingly.