The most important question which you must ask yourself is Am I the author of the theme or plugin?. If your answer is yes, and you are responsible for the up keep of the plugin or theme, go ahead and change it and modify as you like.
If your answer is no, then you should not make any changes to it, not even a small thing as a simple dot .
. The same goes for WordPress core files. The simple reason being, as you’ve stated, if the theme/plugin/core is updated, you will lose whatever you have done to the theme/plugin/core.
I would recommend that you create your own small functionality plugin with this extra functionality. It is quick and easy, and will save you many tears later as it will not be overwritten unless you do it yourself.
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