I have the same problem. It is not only the CSS Pointer setting which doesn’t apply, also other hover actions like menus. This was already posted:
https://www.nomachine.com/forums/topic/physical-screen-hovering-over-chrome-links
I run Chrome 39 and it is still there 🙁
Details:
Server: Arch, package ‘NoMachine’, version 4.3.30-1
Client: Mac Yosemite, version 4.3.30