To discuss your example, it helps to distinguish between petite caps who have roughly x height and small caps, who are larger than that (but not as big as regular caps). What you have, strongly looks like petite caps or anyway too small for being used for acronyms and similar. Text using them will be awkward to read, because the brain will automatically parse these acronyms as lowercase, even when they should not be – because they are proper names or are at the beginning of a sentence.
If the font in question does not have distinct small caps with these properties, I would refrain from this convention altogether.
That being said, a very good font would also have extra variants of numbers, brackets, slashes, etc. specific for all-small-caps style that are specifically designed to not stand out from your small caps.
If these are not available, possible solutions for your problems are:
Use lowercase numbers as their centre of mass is roughly the same as those of the petite caps. However, they will still stand out a bit due to most of them having ascenders and descenders.
Use specific glyphs for Roman numerals.
Use suiting alternative forms where you can.
To illustrate some points, here are your examples set in Linux Libertine (which has rather small caps than petite caps), using lowercase numbers, designated glyphs for Roman numerals, and alternative characters:
Finally, since we are talking about typesetters for academic journals here, I strongly suggest investigating the what features the font they use supports (they won’t use any other) and give them detailed instructions on what features you want (and even then you only have a tiny chance of success). The best way to go would probably to just settle on regular all caps.
Use a smaller font for the joined digits and symbols
Unless you have optical sizes available, this is a bad idea, since the scaled glyphs will not optically match. This is the problem with faux small caps, faux super- and subscripts, and similar.