Personally I don't think mods have to change much at all.
The new hopper is still buggy as hell from what I've read on the wiki and way inferior to anything RP2 or BC pipes offer in control and management (and speed for that matter). It looks good enough to catch drops from automated farms, but I seriously doubt you can build any decent sorting or auto-crafting system with it. Also, with 1 Glass + 2 Cobble/stone/etc. = 8 pipes those hoppers are way too expensive to replace piping from a cost perspective.
For loading carts, I dunno, I haven't spent much time looking into Railcraft, but I doubt it'll make the whole mod obsolete. I think Railcraft will still offer more control over your minecarts and there is of course the whole Boiler and power generation side of it which will always remain a very strong point of Railcraft for many players.
As for new redstone mechanics, how exactly are they different? As far as I can see it's mostly bugs getting fixed and things like BUD switches which are broken (but replaced with various detectors to fill that gap). Maybe I'm missing something, but to me that looks like a good thing (at least for vanilla players). Red Power will (perhaps break and) have to adapt or stick with the old mechanics (I don't know how it's coded and if that's possible or not, but those look like the most logical options to me). If Red Power can stick with the old mechanics it probably will, at least at first.
As for Nether quartz, personally I hope it stays out of mods as much as possible or that mods provide a way to fabricate it. I honestly don't feel much for starting yet another new world just because some vanilla ore got added with little to no purpose. To me it kinda feels like a magic detection ore, which in most mods is actually done by creating actual circuits and expensive components, which I prefer over just digging up a simple ore.
Overall I think the 1.5 update will be a good one and perhaps certain parts of mods will get contested by vanilla items/blocks, but personally I don't see much reason for mods to remove the components that get vanilla equivalents. Mostly because most mods will always have the advantage that their own components interact a lot better with the other components of the mod, which as a whole will offer a lot more flexibility and control than most vanilla components cobbled together.
In the end we'll have to wait and see though. This is just my view and opinion on the matter, I don't know what modders and other people think though.