Modified ElGamal encryption (ElGamal encryption with messages in the exponent ) is implemented in a pairing friendly elliptic curve. Is it secure?
Yes! Good observation! Although note that the original Helios paper by Ben Adida does not mention such implementation details, i.e., on which curve to instantiate the ElGamal encryption scheme.
Your observation basically stems from the fact that the decisonal Diffie-Hellman (DDH) assumption does not hold on pairing-friendly curves. On the other hand, one needs to assume the DDH assumption for the semantic security of the applied ElGamal encryption scheme. Therefore, the choice of the ElGamal encryption scheme implicitly implies that one needs to choose a suitable group, where the DDH assumption holds. If a pairing-friendly curve is chosen, then DDH does not hold, hence also the semantic security of the ElGamal encryption scheme is lost.