1. It has no negative effect on frequencies.
2. The foot bath frequencies transfer through water, no problem - or it wouldn't ever work. It is only an annoyance that water gets inside the cylinder, but no harm is done by it.
If you want to, you could take the rubber ends off of the bottom (or top) to make emptying the water and allowing the cylinders to dry more easily. Just be careful in case the ends of the metal are sharp.
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