A non-experts opinion:
By dropping the water in your tank and filter, it will still get picked up and moved through the system just by the vibrations and road bumps. Long term it may have more of an effect.
By emusifying, you are bonding the water to the fuel. So it does not send a blob of water through. This happens on a very small scale. In my opinion, it is such a small scale your injectors would not see any effects from this. And again, emusifiers will not pick up tons of water. You get a bad tank and it will not bond it all to the fuel.... Try it in a glass, put mostly fuel.. some additive.... then add water, mix it up...... see how much water it will take.... Make sure to do it drops at a time... cause it wont bond much..... add more additive... see what happens....
Getting it out is much better in my opinion than leaving it there....