Interesting, I wonder to what extent this could impact the transparency of individual transactions.
The impact goes most likely in the other direction some may think. Because the connection between signatures and previous transactions to the participating UTXOs/addresses is not lost with this technique.
The problem is that not in all types of transactions the signatures can be aggregated via CISA. Thus, as the incentives should direct people into using it to save fees, eventually there will be very few non-CISA transactions left. And these would then be special cases like atomic swaps (a decentralized technique to exchange BTC to another coin) using adaptor signatures -- which is just a technique which was invented to improve privacy. Adaptor signature atomic swaps currenty don't tell the chain analysis folks / authorities that an atomic swap has been made without additional data. But if those txes are the only non-CISA transactions, chain analysis companies could perhaps use this to isolate atomic swaps and mark them as medium/high risk.
Private atomic swaps is imo a very important technique which should not be sacrificed lightly.
On the other hand, as it was already posted here, you have a fee saving effect on CoinJoins, and this means that using CoinJoins will be cheaper in most cases than not using it. In theory this should also align the incentives that everybody uses CoinJoins, at least with half-agg which doesn't require interactivity. If really everybody used CoinJoins this would make Bitcoin almost as private as Monero. And that would of course be a big win - if this is the outcome, then the problem with atomic swap privacy is almost negiglible because you would simply CoinJoin the previous/following transactions anyway.
The problem is that many users may still be scared of CoinJoins because they fear the coins being seized by some exchanges. And if these people are the large majority, privacy could be even lower than before CISA.
Doesn't want some altcoin implement this first? Let's say LTC or Dash (as they're BTC-based and could simply use the draft BIP for half-agg)? This would perhaps show us the real life implications on privacy.