Why are the extension cards in separate stacks?
I've deleted my previous answer as it was based on too many wrong assumptions on my part!

When playing with the Catan Card Game Expansion set, you could choose to just mix all the expansion cards together into five stacks as normal.  I don't think this would break anything, as such.

However, it strikes me that the new Themes introduced in the Expansion set would be quite significantly diluted by just being mixed in with everything else.  Depending on the outcome of the shuffle, your game might not end up being very highly "themed" at all.

By giving the new cards their own dedicated stacks, you give players the option to have a game that is quite heavily based on the theme. (They can, at their discretion, just keep drawing cards from that stack, after all.)  This could be particularly relevant if cards within a theme work better with each other, instead of in isolation: and I'd be amazed if this was not the case - most boardgame expansion kits I can think of are designed to have new internal synergies, rather than just complementing the mechanics of the basic set.