1 atmosphere air pressure is somewhere around 10 metres of water � the vacuum cleaner need only generate 0.1 of an atmosphere of �suck� to �lift� the water 1 metre.
Therefore it is highly likely that the vacuum will suck up most of the water in the toilet bowl. What will then happen to that water will to some extent depend on the design of the vacuum cleaner (bagless/bag/hepa filter etc).
But I would guess that a fair quantity would be expelled from the vacuum cleaner via its exhaust. I doubt if any of the water (a relatively small quantity) would penetrate the dust seals and get to the windings of the electric motor, but I could be wrong.