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We have a relation between Electric field(E) and potential(V) as

E = -∇V and V = -Integral (E)dl

In such case, V have to be equal to -E.D ::: V = -E.D but in most cases we use V=E.D. Why is this?

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Think of it like this: -

enter image description here

Ignoring the negative sign is done quite often and this slightly corrupt act is also seen in magnetics (V = L.di/dt) instead of the version with a negative sign.

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The correct expression is the first one

https://en.wikipedia.org/wiki/Electric_potential

You use the second one only if you just care of the absolute value.

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