Are alien spacecraft likely to have toilets?

“assuming they are something like earth’s humans”
– So, yes.

“Or is it more likely that their anatomy is more advanced than ours, and may not produce waste?”
– I’m going with a very confident no, given the assumption above.

On the other hand, if I take your question literally, I’d say there’s a good chance that an alien spacecraft, wouldn’t have any physical aliens aboard it, so then it wouldn’t need a toilet. Unless it was for storing humans, or well-trained animals.

2) If they did their research well, and the craft couldn’t get home quickly enough that it wouldn’t matter to much to them, then yes the craft would want a toilet, and a way to recycle the waste. Whether the planet they took the humans to would or not, would depend on the timing, communications, and how long they had to think about it, how much they cared, etc.

But it really depends on the aliens. For example, some might be capturing the humans, in order to consume the human excrement, as a delicacy.

Others might prefer to install a bypass tube in the humans.

With unspecified aliens, all bets are off.

No, they just beam the waste out of your colon into the food processing system for sterilization and re-integration into the Chili. Waste nothing.

All organisms produce waste, whether it is solid, liquid, or gaseous. It needs to go somewhere.

1. If they create waste, perhaps they can recycle it, to a degree. Like we recycle urine in space.
Or. I actually strongly believe that only artificial “life forms” actually travel with some type of propulsion. No creature could endure the inertia all the acceleration and deceleration. It’s likely that all life, is mortal.
So. They would have to have a way to hibernate or freeze themselves to survive long trips.

Aliens, that use propulsion, would be robots or androids. Either pre-programmed and/or an AI. Or, being controlled by the actual aliens on a planet, maybe even in comfort.

IF. If they can manipulate space and time, AND there are ways to maybe move from one dimension to another, now we’re talking about a craft, that could have actual live aliens on board.
I believe that those vessels would be fairly large. Likely, the vessels would bring the alien’s environment with them (like we do,) and would probably have whatever “amenities,” as they need.
Some reptiles, on Earth, can take very long periods of time to digest their meals. Aliens could maybe “hold it,” for long periods of time.

If it is a research vessel, that was designed for trying to keep different lifeforms alive, they would have SOMETHING. A hole, is all we have in many places. I don’t think I could poo, on an alien toilet.
Unless they plan on establishing a relationship with us, the minimums would suffice.

There wouldn’t be much reason to keep us alive. Perform dissection and examination, perhaps store the remains for further study.

We’re just monkeys, playing civilization. We’re likely pretty low, on the universal intelligence scale. We can’t even live together.

I just can’t think, of many reasons why aliens would care about Earth.

Yes. Because, even with aliens, shit happens.