Is there a public key semantically secure cryptosystem for which one can prove in zero knowledge the equivalence of two plaintexts?
Yes.  Such proofs are possible for El Gamal.

It involves a zero knowledge proof of equality of a discrete log, together with the homomorphic property of El Gamal encryption.

Recall that given $E(a)$ and $E(b)$, anyone can form $E(a/b)$ using the homomorphic property of El Gamal.  Suppose $E(a/b)=(r,s)=(g^k,h^k a/b)$ (where $g$ is the generator and $h$ is the public key).  Then proving that $a=b$ is equivalent to proving that $a/b=1$, i.e., that $(r,s)=(g^k,h^k)$ for some $k$, or in other words, that $(g,h,r,s)$ is a Diffie-Hellman 4-tuple.  There is a standard zero-knowledge protocol to prove this fact.  That's all you need.