You're right, totally exposed lava lamps in a carpeted lounge make for a far more realistic portrayel of a matter/antimatter reactor and it's engineering assembly.
At least it represents a bit more of the clean-room aspect you would expect in such an environment. And you can actually justify having the transparent rig so as to provide visual inspection of the flow. It'd be like having all the medtools of the time, but the doc still taking your pulse by hand, because he can gauge by his natural senses as well as via tools.
Don't see how you can justify the 20th century pipe fittings in any 23rd century context, or why you would want to.