What is the best technique I can use to encrypt inner nodes in B+tree?
We don't know your scheme, so we cannot say which technique is better for you, but in most earlier schemes that use binary vector (or any integer vector) for store information, Secure Inner Product is most used tools for encrypting! And it's useful for searching in some condition and depend on search construction.

P.S. Why you using bloom filter that has false positive issue?
I'm working on SE too.