I'd say this is almost certainly the case. There's one (though only one) episode of Yu-Gi-Oh! where Yugi is actually shown buying and/or trading for new cards, one of which ends up being crucial in his next duel. Which is a bit weird now that I think about it, since that particular show usually treats "rare cards" as somehow not things that you can just walk into a store and buy.
As for the original question of "How much does the main cast spend on their decks," CCG prices are almost always far more demand-driven than supply-driven, which means that being even the highest rarity doesn't guarantee that a given card will cost more than a few bucks (and in fact, at least in M:TG the relationship between how rare a card is and how good it is is fairly loose in the first place). Combined with the fact the associated media franchises always leave the competitiveness of a given deck entirely up to the plot, and I'd actually be surprised if any of the protagonists thereof had an appreciable budget (barring characters such as Seto Kaiba where the fact that they can afford any card they want is the whole point).