You should be able to but it would depend on the condition of the wood used and how the crates are assembled. If the two pieces are not cut square, it could cause the joint to not pull tight or pull at an angle. Would you happen to have a picture of them? I would be able to give you a little better idea if it would work or not.
Thanks for asking for my advice, unfortunately I have only just purchased a kreg jig and am still trying to get the hang of it (a kreg virgin if you like lol). Sorry can't be more help, good luck on finding the answer to your question.
Kind regards Dave