In general I've found guardian spawn mechanics to be extremely inconsistent but just as I came up with a fairly efficient farm design the game just proceeded to confuse me more. The issue is that when Guardians jump out of the water without ending their swimming animation they continue to swim midair. I'm not sure what the exact conditions are to recreate this bug but I do know that they ARE capable of flying or "Swimming in air." I highly encourage that the devs look into this.