If it comes to continuing to use lava and water (and any variation thereof), it may become a necessary game mechanic, to encase these elements of the ship in a transparent/translucent set of blocks to get the continued effect without the effect flowing away or otherwise creating a mess.
Example: While for now you can have lava thrusters exposed to space, in the future, you may have to enclose those lava thrusters in glass slabs to keep from having a messy "spill" falling out the back of your ship. On the other hand, depending on how flow is handled, fluid flows may be used by creative builders to create new special effects. (liquid thruster plumes that reach out the back of the ship or liquid pipe contents that flow up or sideways, etc.)