SEE NOW THT V HAVE MODIFIED THE QUESTION AND WE R WITH THE EQUATION

now if u observe carefully u will find tht
is a scaler quantity not a vector. for this u can refer to the basic formula of flux tht is given by

thus we can see tht flux is a dot product or scaler product of two vectors namely electric field vector and area vector. Thus now we can say tht flux is a scaler quantity. now if u look at the equation referred in ur question, u will find no contradictory thing. all the quantities involoved are scalers and there u are with no problem at all regarding vector.
PLZ.... VOTE IF SATISFIED WITH THE EXPLANATION.