A 90° diagonal will generally be considerably more comfortable for astronomical use. Also, all other things being equal (and they never are) a 90° diagonal will be more likely to provide a higher quality (sharpness, contrast, freedom from "artifacts") view; but that difference may or may not be quite subtle -- if noticeable at all. Consequently, astronomical observers tend to favor 90° diagonals.
That being said, I would suggest you purchase the telescope you want, based on other reasons, without regard to the diagonal it comes with. Either telescope should be perfectly usable with either diagonal. If your preferred telescope doesn't come with your preferred diagonal, you can always purchase the other diagonal separately -- and enjoy the option of using either diagonal depending on how you're using the telescope (for example, astronomically or terrestrially).
Note: Some diagonals, of either type, if cheaply made, may vignette the views with low-power, wide-angle eyepieces due to an under-size mirror or prism (to save cost). This is more common with the 45° diagonals; but is sometimes found with the cheaper 90° diagonals as well.
P.S. I have both, 45° and 90° diagonals of various sizes and image orientations, It's very rare for me to use a 45° diagonal for anything. For myself, the preference is primarily a comfort issue.
P.P.S. If I want a "correct-image" (as opposed to a mirror-reversed image) I'm more likely to use a more specialized, 90° correct-image diagonal than a (more commonly available) 45° correct-image diagonal. This time, my preference is due to both, comfort and quality.