This is a wrong interpretation. Physicists have a shit-ton of models that produce "aphysical singularities", they just work around those to get meaningful answers anyway. This is a whole trope and stereotype. Some of the most successfull and accurate predictions in all of physics come out after you discard a bunch of singularities.
See e.g. https://en.wikipedia.org/wiki/Renormalization
Nobody who actually works in fluid dynamics on any sort of application gives a hoot about the N-S millenium problem. Many do not even know what it is. There is no practical effect of this proof on how we do fluid mechanics.