Footnotes effectively have no place in CS, engineering or natural sciences. Other disciplines treat footnotes very differently, I think.

This is certainly too strongly worded to be correct. I use footnotes quite a bit in my papers (physics) as a strategy to handle the "two audiences" problem - that many or most readers just skim for main ideas, but some (and those whom I might argue are more important) try to follow the details closely. I presently use footnotes for the latter audience for certain supplementary details or technical qualifications that would break the reading flow or add unnecessary length for the former.

I do appreciate the arguments that footnotes can be distracting, or that one doesn't know whether to skip them, but at present I see them as the best option for keeping the main body streamlined/as short as possible without sacrificing points that I'd like to make that wouldn't make for or fit into an appendix.

I disagree completely. There are many different sorts of works you can publish relating to a given field, and some of them benefit from the asides and additional context that footnotes can provide, particularly pedagogical works targeting an audience of a wide breadth of experience.