... and Whatsapp uses FreeBSD extensively. Could this affect the end-to-end encryption that Whatsapp uses?
At around 23:50 in the video, Rick Reed talks about slide #17, they say they are running 9.1 - 9.3, and looking at 10.1 (not in a hurry as 9 works for them).
[1] https://www.youtube.com/watch?v=TneLO5TdW_M
[2] http://www.slideshare.net/iXsystems/rick-reed-600-m-unsuspec...
All of those freebsd versions you refer to (9, 10) are part of the production release cycles and thus are not -CURRENT.
If whatsapp uses 10.1, then they are NOT using -CURRENT
Theoretically, WhatsApp could generate the keys and forward them to clients, and you could still plausibly call it "End to End"