Adrian,
The problem with your method is that the film's emulsion absorbs a certain amount of water - and anything else that is dissolved in it. All the water on the negative doesn't just run off leaving a dry surface; the absorbed water must evaporate from the emulsion, leaving behind everything else that was in it to begin with. This means that there is likely some residual acetic acid in your negatives' emulsion, which can't be good. Baby shampoo may be harmless, but who knows? PhotoFlo is a surfactant that was designed and tested to work on and not damage photographic emulsions. It may even be cheaper than baby shampoo too...
The ephemeral problem of water marks has to do with the myriad of causes of the problem. One can get water marks from using too much of the surfactant (e.g., PhotoFlo or the like) in the final rinse, or by not hanging the negatives so that all the surfactant-laden water sheets off. If the water collects in a puddle and then dries, it leaves behind too much of the surfactant, causing marks. Also, if one mixes the surfactant too dilute, the sheeting action of the surfactant is not complete and droplets will form. This also results in droplets drying and thereby concentrating the small amount of surfactant in them, causing marks. The right amount of surfactant and hanging the film properly will fix this part of the problem.
Another common cause of water marks is dissolved minerals. In areas of hard or mineralized water, these minerals get into the film's emulsion and when the film dries cause mineral deposits to form on and in the emulsion. The solution here (pun intended) is to soak the film in distilled or demineralized water long enough for enough ion exchange to take place so that the retained minerals in the emulsion are negligible. This step is commonly combined with the surfactant step, in which case it needs to be lengthened to include the needed soaking time to leach the minerals from the emulsion. This time is dependent on water quality and must be determined individually. The final distilled water bath (with surfactant or not) cannot be overused or the level of dissolved minerals in it will reach a point where too many minerals get left in the emulsion. I use my distilled water/surfactant bath one-session.
Finally, there is the somewhat random problem of uneven drying, which seems to bother some more than others and some films more that others. When droplets form on the film's surface (i.e., no surfactant or not enough), the areas under the droplets will dry at a different rate than the rest of the emulsion. This can cause some stress and stressing of the emulsion at the interface of these two areas, sometimes causing rings that correspond to the perimeter of the droplets (or streaks if there are runs on the emulsion's surface). I would imagine that films with less hardening are more susceptible to this than others and that drying speed plays a significant role here. Solution: use a surfactant properly.
As for squeegeeing: stripping the excess water from the film surface isn't in itself a bad thing. However, if the emulsion is fragile or the squeegeeing too vigorous, the emulsion can be damaged. The risk of not squeegeeing is that water will bead up or form runs on the negative and can possibly lead to uneven drying marks; the danger of squeegeeing is that one can scratch the film. Solution: use your surfactant properly so that the water sheets and runs off the film evenly and if you prefer to squeegee (like I do), make sure that you have a method that is gentle enough so as to not damage the film you are using.
Finally, keep dust and particulates off your film from beginning to end of the process and hang your film in a dust-free environment to dry.
Best,
Doremus