It seems fairly certain there will be a 6" Nexus, but there's also been plenty of rumours for a 5" one too, though what the differences will be is anyone's guess currently.
If you like the current N5 2013 don't be put off though - it's a great phone and I can't see any 5" 2014 drubbing it. It might have a bigger battery but I expect anything else will be negligible - and the N5 2013 will get Android L anyway, which is where the biggest change will be.... and if the 6" leaks are anything to go by the N5 2013 will look miles better than the 2014 model(s).
You'll have to get an N5 2013 soon though as stock is already dropping and it won't be replaced.