Hi,
I think they are reliable. After having a quick look in the code, it tries to find such elements but uses a default value if they are not present.
I think the message is a bit to frightening. Probably it would be better to set it the level from WARNING to INFO.
And I actually wonder why the information is looked up, if it is not necessary.
Maybe @kraftek and @obarrilero, the developers of this module can give some insights.
I my self will have a look at this message
SEVERE: org.esa.snap.core.gpf.internal.OperatorSpiRegistryImpl: org.esa.s3tbx.watermask.operator.WatermaskOp $ Spi: LandWaterMask conflicts with org.esa.snap.watermask.operator.WatermaskOp $ Spi: LandWaterMask
It is also not harmful but it tells me that the LandWaterMask operator is registered twice. So there must be something misconfigured. But it will cause no problem.