It is totally normal for an inch or so of water to be in your hull. The bilge pumps in these things operate on the peri-jet or eductor principle. Tubes that run through to your pump, create a vacuum on the bailers when the nozzle is providing thrust. When the motor is at idle, if the bailer tubes are not attached high up to the inside of the hull, they might leak a little water pass them. Also, as mentioned, the thru hull seal, especially in older models, will normally leak by a little water.
But, for the one that was worried about sinking..... It is very hard to sink a jet ski. They are designed with stryro foam inserts that line the sides and bottom of the inside hull. You can fill it up with water and it will still float. I don't think I'd try and start it with that much water, but you won't sink it.