There can be more to it, and often is, but I don't see anything that suggests there has to be more to it. For some nouns, -Hom might suggest things besides size, because they're the sort of noun that has a lot of "variables". For example, words referring to living things not only have size, but also maturity as a characteristic distinct from size. In this case, it might be preferable to use mach instead of -Hom if you mean "small", because there are other aspects of the noun that could be "lessened" that you don't intend to.

On the other hand, some nouns are just mundane objects, and size might be the only variation among them. Like these two:

It's just translated as "small scoop" in KGT (and bo'Dagh'a' is translated as "big scoop"). In this case, it seems clear that -Hom just means "small" by itself. Scoops don't really vary in terms of importance or intensity or maturity. They're just scoops.

A naQHom is mentioned in KGT as the small stick you hit an 'In with. It's just a small stick. A twig would be a naQHom, but not all naQHommey are twigs. Like I said earlier, I think part of this issue is because it's easier to give different English glosses for words with -Hom on the end, giving the impression that there's some underlying conceptual difference. A DoQmIv is a basin or container for holding water, and a DoQmIvHom is a small basin or container for holding water. But since DoQmIv was originally glossed as "sink" and DoQmIvHom was glossed as "something like a bucket", we start associating -Hom with the differences between a sink and a bucket (not fixed in place, no faucets, no drain), rather than understanding "bucket" as an example of the size of a thing that is a DoQmIvHom.