I'm not sure about dilithium: if it takes a lot of energy or time or computing power to replicate it, Janeway would go for every opportunity to obtain it by other means, such as trade or direct mining. And it's not as if our heroes in VOY, TNG or DS9 really ever run out of dilithium, or go actively hunting for it. ("Demon" has them hunting for deuterium instead, which is a poor choice treknologically, but there you have it).
However, you make a good point about the gel-packs. If a well-equipped starship that in a previous episode was capable of replicating new neural tissue can't do those, then it might be that they really are unreplicable overall. And AFAIK, this is the only time in Trek when something is directly stated to be unreplicable (without the specifier "in our current predicament", as was used in TNG "Night Terrors").
One might of course argue that Janeway would be the sort of skipper to first run out of spare gel-packs and then start worrying about the fact that the lack of gel-packs makes the replicators inoperable.