The Popping and the Water
Your two pictures, especially the second showing the bonding, and the your description about the knocking are revealing, and they are related.
The second picture shows large voids in the cement/thinset. Floor tiles must have more than 80%, preferably around 90% cement fill and bonding, where the voids are sporadic, small and isolated. Your pictures show much less total contact, and large contiguous voids.
Troweling
It looks like the tiles were not set with a correct combing of the cement, and instead blobs and/or scrapes of cement were applied. This blobbing might have been an attempt to even the tile surface where the concrete floor dips, but it was not done correctly. To compensate for dips there should have been a base of self levelling cement applied first, or a different trowel used locally with coarser gaps for more cement deposit.
The main problem with large voids is poor support for the tile, leading to tiles cracking under heavy and hard drop loads (dropping pans, jars and bowling balls). Clearly this has not yet happened, even in a drop-prone area of the kitchen.
Bonding
The popping sound effect has a different cause: the tile is not bonded to the cement, causing it to deflect and/or to teeter totter where there is even the slightest amount of play between tile and cement. The primary cause of this is poor bonding of the cement with the floor, or more likely, poor bonding with the tile. Thinset comes in different varieties, where some are suitable only for certain backings (concrete vs. plywood) and certain tiles (ceramic vs. porcelain).
Thinset for ceramic tiles cannot be used for porcelain tiles or even for some floor-rated ceramic tiles. This has to do with the amount of polymers in the cement and the porosity of the bottom of the tile. Dense and less porous tiles require a high polymere tile thinset cement, which is far more expensive (double-ish) than regular tile thinset. In an attempt to save cost perhaps a lower grade not suitable for the denser floor tile was used.
Even with the correct thinset, the unfinished concrete floor and the tile's back still require a wetting or keying of the surface, where the cement is worked in before it is troweled, on both surfaces. Omitting this step can cause poor bonding between cement and floor or tile. The ensuing micro-gap can give the tile just enough play to flex or teeter-totter resulting in the plopping sound.
Water
The water ingress under the tiles is just a secondary symptom and not a cause: water permeates the grout or any pin-hole imperfections in it, through capillary effects and gravitation, and simply remains in the deep pockets under the tiles where it has little or no chance to evaporate.
The source of the water could be condensation on the tiles, water from mopping, spills etc...
Unless your kitchen experiences a freeze/thaw cycle (unlikely), the water is not the cause of the damage, but a result of poor installation.
The Solution
You can try to limit your fix to the problematic tiles only.
If the installation is poor enough, you might be able to carefully lift the tile with a crow bar or other flat lever. Work it by wiggling so that the tile does not flex excessively but so that the cement fatigues and releases its bond where it is still attached. Do this after scraping out the grout.
Then reinstall the tile with the correct thinset for the tile type, using the correct keying and troweling technique.
Where this fix is not possible, using epoxy grout can be used to stop the popping and water ingress. The tile will still lack proper support, but this does not have to be a problem since the tile has so far held up to the typical use and abuse in that area of the kitchen.
It is important to let as much epoxy grout as possible flow under the tile and provide some bearing to stop movement and not just side bonding. For this, as you scrape out the grout also try to scrape out a some cement under the tile, as an upside-down T, even if just a millimetre under the edge of the tile.
