I don't know about water affecting scents, I suppose it could dilute the scent somewhat. I heard from a sales associate working a department store fragrance counter that soaps can affect a scent, but I haven't had much problem in that regard. I would say if can, wait until your skin is completely dry to apply cologne and you should be fine.
I tend to think in all reality the scent from most soaps will be overwhelmed by the average EdT.
Having said that, I do have a fair number of soaps/gels matched to scents which does seem to help extend the scent a bit.
When not using a soap matched exactly to scent, I do tend to use a soap that is somewhat neutral, or in the same basic scent neighborhood as the scent.
Overall, unless the soap you use has a strong scent of its own like perhaps Irish Spring, it likely won't interfere with your EdT.