If you pick up more than 24 heart containers in the game itself, they'll work fine.
If, however, you try to set too-high numbers in the init data or cheat menu (the H.Containers dialog, or in the Items tab of the Link Data dialog), they'll be knocked back down to 16 or 24 (whether 16 or 24 depends on whether or not the "24 Heart Containers" quest rule is checked).
...I could've sworn this was fixed earlier. <_<'