If you throw an ender pearl that's the only one in its stack, the cooldown is not applied. You can immediately throw another ender pearl in a different stack.

How to reproduce

1. In survival mode, get two stacks of two ender pearls (total of 4)
2. Throw one (notice that both stacks go on cooldown)
3. Throw one again (the last one in the stack)

Expected results
Should go on cooldown again

Observed results
It doesn't, you can immediately throw another pearl