Condensation is not just possible but would happen by default. You described the tubes as steel lined with aluminum in contact with the ground, if not buried. That’s going to be consistently cool enough for passive condensation.
Getting water out of a long tube shouldn’t be hard with multiple drains, and if there’s any incline, you just need them at the bottom. You can just dump it in the ground. Use a plumbing trap to keep the gasses separated. They’re at equal pressure, so this should work, and the pressure can also be maintained mostly passively with hydrogen bladders exposed to the atmosphere on the outside, although the burned hydrogen will have to be regenerated before they empty completely, but this can be done anywhere on the pipe. Hydrogen can be easily regenerated by electrolysis of water, which doesn’t seem any more expensive than charging the batteries. It might be even cheaper to crack if off of natural gas or to use white hydrogen when available.
Are turbines more expensive than electric motors for similar power? It’s true that conventional piston engines are heavy, but batteries are also heavy, especially the cheaper chemistries.
Alternatively, run electricity through the pipe to power the vehicles so they don’t have to carry any extra weight for power. It’s coated with conductive aluminum already. If half-pipes could be welded with a dielectric material and not cost any more that would work. Or use an internal monorail, but maybe only if you were going to do that already. Or you could suspend a wire. That’s got to be pretty cheap compared to the pipe itself.
Hydrogen can only burn in the presence of oxygen. The pipe does not contain any, and combustion isn’t possible until after they have had time to mix. It’s also not going to explode from the pressure, because it’s the same as the atmosphere. The shaped charge is obviously going to explode, that’s the point, but it will be more directional. That still doesn’t sound safe in an enclosed space. Maybe the vehicle could deploy a gasket seal with airbags or something to reduce the leakage of expensive hydrogen.