Why do some science journals capitalize the words in a title, and others don't?

Essentially, the way to check is to look at if the particular journal to which you want to submit a paper uses title case or sentence case for the capitalization of titles. I think a lot of it is publisher-specific. For example, in my field, I publish primarily in American Chemical Society journals, which use title case, and AIP/APS journals, which use sentence case.

It really doesn't matter. The copy-editors will fix that kind of thing for you.

If you really must know, look at the journal's author guide or examples of papers in the journal, on the journal's website.