How thick are Dominion cards?
I just did a measurement of my fairly well played dominion cards.

When allowed to float up, a stack of 50 cards is 23/32 of an inch tall. I tried different combinations to account for imperfections and came to this number multiple times in various trials.

When compressed with a gentle hand to maximum compression, they compress to 21/32 of an inch for 50 cards.

Thus if you were to have a box holding 500 cards I would expect them to be at absolute minimum 210/32 of an inch, or 6 9/16 inches. If we allow for comfortable float compression that would take us to 7 3/16 of an inch. Since you'll want at least some wiggle room, I would suggest making your 500 card box of dominion 7 inches long. Keeping in mind that 500 cards is 50 types, you may want to calculate extra room for things like placeholders, extra cards, separators, etc.