1-How does the UTXO get stored eventually in the UTXOS set?
Is it in its we could say encrypted or obfuscated form, or what?
I mean no mention about public reveal to all, what if it's dust value for example?
Or how the continuous data analysis sites consider it? in what range of values?
I'm going to answer how it can be done on a Mimblewimble model which can be thought of as state of the art Confidential Transactions. Yes, an output is just a Pedersen commitment so you can't see the amount.
Looking at the output, you can't tell if it's a dust value or not. One interesting fact about MW specifically is that you can get rid of dust attacks completely because the receiver is involved in transaction signing so you can't get a dust output without signing the transaction yourself.
2-What about the fees?
Most of the EQs are based on input= output, how do we put the fee and how will miners know a its value?
-Is this the case I previously encountered in a paper where a UTXO must be dedicated to the fee in each TX?
-Even though, miners should know the fee in advance to decide whether or not to select this TX, so how?
I'll be talking from the Mimblewimble point of view. You can put it as a metadata along with the signature. The signature itself can sign for the fees that come with the data so anyone can verify and the miner can add the missing fee amounts to themselves by creating a new pedersen commitment coinbase output.
Sorry if these are not helpful, but I only understand MW and don't really know the details of the original CT proposal.