Higher compression ratios mean higher temperatures. Higher temperatures means more NOX in the output. As it is cars _already_ have to run richer than stoichiometric in order to keep from melting the catalytic converter. I would expect this will require some extraordinary pollution control measures as well.
There's plenty of ways to get temperatures down. Bigger intercooler, even refrigerated intercooling, water or water-methanol injection in various forms, going to high alcohol content fuels, etc. Even putting a waste heat recovery unit (WHRU) between the manifold and the catalytic converter is doable.
If you want to get really crazy, imagine a WHRU on the manifold in the form of a Rankine cycle where the expander drives a compressor for the air inlet. Like a thermal turbo, if you will, giving you more charge air than NA but with much smaller parasitic power losses than a mechanical turbo.
