I've been running dual boot setups for more than 3 years now, on two different machines (laptops), with:
- Windows 8.1 alongside Ubuntu 12.04
- Windows 8.1 alongside Ubuntu 14.04
- Windows 10 alongside Ubuntu 14.04
- Windows 10 alongside Ubuntu 16.04
So far I have not had any issues with any updates and I have regularly updated both Windows and Ubuntu.
On one of the machines I even made the (then free) upgrade from Windows 8.1 to Windows 10 and everything still works fine.
EDIT:
FWIW I never used the "install along other operating system" option during Ubuntu setup, but preferred to manually create the partition scheme. Obviously, if you choose to do this you should be super careful not to erase the Windows partition.
The two issues I ran into while using a dual boot setup were these:
- BIOS clock conflict. The link also provides an easy way to fix this problem.
- Problem mounting partitions that are also used by Windows. This can easily be solved by turning off the Fast Startup option in Windows.