You would only use "hypothetical" in this context if you were referring back to something that had already been mentioned, ie that had already been established as being hypothetical.

Since, in your text sample at least, NASA's wishes have not been mentioned, you're referring back to something that doesn't exist, and this will cause confusion.

As @silenus suggests in the comment above, "presumed" is a better choice as it can be used with no prior reference to the wishes: the speaker is saying that they "presume NASA has these wishes".

You would only use "hypothetical" in this context if you were referring back to something that had already been mentioned, ie that had already been established as being hypothetical.

Since, in your text sample at least, NASA's wishes have not been mentioned, you're referring back to something that doesn't exist, and this will cause confusion.

As @silenus suggests in the comment above, "presumed" is a better choice as it can be used with no prior reference to the wishes: the speaker is saying that they "presume NASA has these wishes".

EDIT - I'm going expand on my answer, since it may not have been clear.

Original text:

“They probably wouldn’t. But, NASA never discovered aliens; this situation is unprecedented,” Mr. Fern continues. We look at Mr. Fern quizzically. There are aliens right outside, trapped inside leak-proof containment cells. “That’s why you’re asking us,” Mac says. “Your team will say no, won’t they, in respect with NASA’s hypothetical wishes.”

Here, Mac is describing NASA's wishes as hypothetical. But what is he talking about? No-one has mentioned NASA's wishes. Describing the wishes as hypothetical here makes the reader think "Err, what wishes is he referring to?". They may then re-read the preceding text, asuming they've missed something. But they haven't.

On the other hand, if there was some mention of what NASA might want, previously, then the reader knows what's being referred to. eg, if I add a sentence at the start.

“NASA wouldn't want us to sign the aliens up with a StackExchange account“, Mac said. “They probably wouldn’t. But, NASA never discovered aliens; this situation is unprecedented,” Mr. Fern continues. We look at Mr. Fern quizzically. There are aliens right outside, trapped inside leak-proof containment cells. “That’s why you’re asking us,” Mac says. “Your team will say no, won’t they, in respect with NASA’s hypothetical wishes.”

Now we know which wishes are being described as hypothetical.

Re-reading the original text, i suspect that there might have been some mention of NASA's wishes previously, which wasn't included in the sample - the first sentence seems to follow on from something along those lines. OP, is that the case?