Can it hurt to include Nekudos (vowel marks) when typing Hebrew? Do all systems that support Hebrew lettering automatically support Nekudos? If not, do they at least degrade gracefully?
Nikudot support has been problematic for a long time, on many applications. I do not know whether Windows magically gets it right, but I know Linux has had difficulties (and many applications still do have difficulties).
Several years ago, I sent a survey of nikudot support to the authors of many important Linux applications (word processors specifically), complete with screenshots. Many of these applications supported nikudot badly, and they definitely did not degrade gracefully. Some of the developers involved took made fixes based on my email, but some fonts are still problematic.
All in all, it's very dependent on what font and what application you use (though application in the major office and creative apps is pretty good these days).
Hebrew Support for Your Browser (last updated: 17 June 2012)
Most of fonts do support nekudos. Necudos are also supported by Unicode.
The programming moves toward Unicode, for example in Java the String object is Unicode out of the box (unlike C,C++,...), so I think that the systems that don't support Nekudos do degrade.
However there are always legacy code on old programming languages (like COBOL) that would probably live forever that don't supports nekudos, but mainly just business logic is implemented that way, the user interface part mostly written on more user friendly languages.
Hope this was not too much programming-oriented answer :)