A carbon dioxide - DVT link? Sure sounds like bunk. Please be careful of spreading medical misinformation.
I have a lot of experience working long days in a high CO2 environment (did my PhD working in volcanic ice caves). IIRC OSHA rules say 5000ppm (0.5%) is the limit for a 40 hr work week (that's more than 10x atmospheric). There is no way CO2 on planes is getting over 1%--- that would cause a lot of health problems. DVT would not be one of them.
If anything would have an effect, I'd guess the relative absense of nicotine in people would be a big part.
Though I thought nicotine _causes_ blood clots, it's possible that that's a chronic effect and the acute effect would prevent them, I'm not sure.