I'm making something a little bit large in decker, and it probably won't be a problem but I just want to know if there's a card limit to be safe. If there isn't a limit are large projects just inconvenient to work with? Or should I not be worried?
I've seen published projects that had around 100 to 200 cards and I don't believe that was anywhere near a technical limit. But I do believe that card management can become a little inconvenient at some point, depending on the project
Just quickly brainstorming some idea to make it easier to find the cards you need while you're working:
You might consider naming cards something identifiable so it's not a list of card87, card88 and so on.
Even forest1, forest2 would make it easier to find things on the Cards list.
Or keeping them grouped approximately to some feature of the project like their location, purpose, chronology, or something else.
Cards can be cut-and-pasted which adjusts their place in the sequence, or re-ordered by dragging in the Card Order menu. (File > Cards)
Sometimes it's handy to do something with scripting that reuses a card, rather than having multiple static cards -- but that depends very much on your project and what you're doing with it.
And even if it's not needed for the final published project, you can use the search engine contraption while making your deck to be able to search for cards that have specific text on them.
(Hopefully someone else has more ideas of how to help. :D It's always exciting to see big ambitious projects come together.)