I assume that the arma3server executable is in /home/arma3 in your case?
In my case arma3server lives in /home/arma3/arma3_server, so i have changed the newRoadShape line to:
newRoadShape = "\home\arma3\arma3_server\a3\map_altis\data\roads\roads.shp";
This does get rid of the error message, but I am not sure if it effectively solves the issue with AI not finding any roads. Since i have an AI patrol mod added to the server which isn't able to work, when it doesn't know where the roads are.
This is an issue which breaks arma3 dedi functionality. So I hope the developers do give this priority.
cheers,
Redd