You gotta understand how replays are stored, and then you'll understand what Famine is saying.
The replay is NOT a file full of movies of your races. There is NO imagery stored in a replay file. It is a file full of data about the cars at consecutive points in time: their position, direction of travel, speed, control position, etc. When you view the replay, all this data is computed and rendered, just like it was during the actual race. Replays are NOT stored on a memory card while you race; those are way too slow to keep up with a real-time data flow. Therefore, having a big empty memory card will have no bearing on the length of replay that can be recorded. The replay data is stored in a reserved area of internal memory until it runs out of space, at which time it simply stops recording replay data displays the message in question. What it had up to that point is available for you to view or save if you want.
Now, understanding that, it's clear that the PS2 can only keep a finite number of data points in memory when it's recording the race for your replay, and that finite amount is not near enough to record an entire endurance race. It's also not necessarily a given amount of time, but dependant on how much memory is available after it's set up everything else it needs to do to run the race, like load track and car data, generate images, maybe frame buffers, whatever it is that has to be done in memory. I haven't examined it (nor do I care to), but it wouldn't surprise me to see that it could record a much longer replay during the Tsukuba 9-hour than the Nurburgring 24-hour.