It won't change the fees at all.

The was Whirlpool coinjoins work(ed) is that they would always pick 2 fresh inputs from Tx0s, and 3 already mixed inputs from previous coinjoins. The 2 inputs from Tx0 were the ones which paid the fees. Every input which was already mixed gets unlimited free remixes. If you look at the 0.05 pool transaction I linked to above (https://mempool.space/tx/f4fd5cad5d4db3716fe2081d1bc20f0beb33a417adf22c8fcca131cb6249adb6), you'll see one input of 0.05014520 BTC and one of 0.05006037 BTC, and the others all of 0.05 BTC exactly. These two new inputs are created from an initial transaction called Tx0 which splits the amount of be coinjoined in to the needed denominations to join the chosen pool, along with a few extra sats in to each input to pay the fee for that first coinjoin transaction. This is obviously an estimate at the time given the current mempool conditions. None of this has changed.

When it comes around to actually joining a coinjoin, before it would always be 5 inputs and 5 outputs, and any extra sats on these two fresh inputs were simply paid as a higher transaction fee to miners. Now if this is the case, the protocol will add in one or more additional inputs/outputs in order to bring the transaction fee down to a more appropriate level.

Nothing changes for the users, except some of their coinjoins now benefit from larger anonymity sets.