I would not use vinegar, as it can be used as a herbicide when concentrated, but will likely be of no value to cleaning if dilute.
Assuming the deposits are carbonates of calcium, magnesium, and iron - most likely with hard water - they really should not be an issue for the plants. They may look bad, but as they will be at the top surface only, they should be of little cultural impact on the submerged roots of an otherwise healthy plant. It is the buildup of fertilizer salts that are of more concern, and that's apparently not what's going on.
Those carbonate minerals can, however, cause new root growth to "shrink back", so all you need to do is dump that top layer and replace it with clean LECA. You can then treat the "carbonated" ones to remove the buildup.
Citric acid is stronger than acetic for that, but a lot of folks swear by soaking in a fairly strong solution of Epsom Salts.
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