What does heterogeneous mean?
Any classification like chemical or a physical change, homogeneous or heterogeneous substance, will eventually fail at one point. From an analytical or physical chemistry's perspective, homogeneous substance is a substance, in a single phase, whose chemical composition is uniform. A heterogeneous substance has different composition from place to place like your garden soil.

Why do we treat a water+water vapour system as heterogeneous in spite of similar molecules present? Also if there exists an equilibrium in the two phases would we still not call them homogeneous?

It is a bad example to label water+ water vapor system as heterogeneous- but with respect to what? It is better to call it a two phase system. You have to define heterogeneous with respect to some property.
For example, if we take tap water in a glass, we can say the liquid (water) is homogeneous with respect to its chemical composition. Let us put some ice cubes in water, now it is a heterogeneous phase, although chemically it is all water.
More formally, from the International Union of Pure and Applied Chemistry's Gold Book:

homogeneity (in analytical chemistry): The degree to which a property
or a constituent is uniformly distributed throughout a quantity of
material. A material may be homogeneous with respect to one analyte or
property but heterogeneous with respect to another.

You can see the subtilty above in italics.