I already see plenty of obfuscated JavaScript out in the wild. Script names have opaque GUIDs and slugs, and the code itself is inscrutable: defining single-character constants and recombining them later, dynamically constructing scripts to be dynamically injected into the page and then run, etc.
I would like to believe that this is done in the name of performance, but my gut tells me this is done in the name of keeping one step ahead of the ad blockers.
As it stands now, I feel that I as a user have no defense against tracking and fingerprinting except by monitoring and controlling access to the DOM at the level of individual operations. I am afraid this is only going to get worse with WebAssembly. "Audit the code yourself" no longer a viable solution except for a handful of experts.
On the bright side, perhaps WebAssembly will lead to fewer ways of interacting with the DOM, which could make it easier to detect malicious/undesired interactions.