I don’t think highlighting is useful. Numerous branches of science have achieved faithful quotations alongside highlighting what the person quoting considers most important without the use of ‘marker pens’. In fact, for centuries colour printing was much more expensive and it continues to be slightly more expensive than black-and-white. Yet the branches of science have survived to date.
I fear, on the other hand, that yet another method of highlighting will be abused by the people who want to see every second word highlighted in a different manner to make sure nothing is overlooked—and that is the main reason why it should not be implemented because it will do harm.
Now how should you point out which highlights were yours in a heavily highlighted text?
A means of emphasis that does not have much effect on blackness is the use of italics, where text is written in a script style, [emphasis mine] or oblique, where the vertical orientation of each letter of the text is slanted to the left or right.
This quotation clearly shows the difference between proper italics and simple oblique typefaces. Ideally, a typeface with proper italics should be used since slanted letters often look less good.