Centrifuges that separate blood spin at a high RPM simulating between 500 and 2000 times Earth gravity. So with your O'Neill Cylinders spinning at ~1G you will still have this problem (when it comes to important minerals settling), but WAY slower.
On Earth, collating of the Ocean is prevented by tidal forces caused by the sun and moon. These forces help keep water churning in a way that it both absorbs and distributes atmospheric oxygen and kicks up minerals for plankton to consume.
The issue with O'Neill Cylinders comes into play when they are tidally locked to thier star and not in orbit of a planet. In this case, there is no significant forces causing still bodies of water to churn and you would still get the hypoxia die off and mineral deprivation you are worrying about, just much slower than you would in a centrifuge, and for slightly different reasons. That said, this can easily be solved for through a variety of means including something as simple as using a staggered re-spin cycle