I believe we mostly considered this to be an acceptable trade off to go to supporting full BB code in report comments now. While clearly there is value in older reports, they likely have decreasing significance over time so the number of times you should need to access a particular URL that is no longer linked should decrease over time.
There are other approaches that could resolve this, though they involve either storing a flag to indicate the mark up type or processing all existing report comments when upgrading to 2.0, neither of which seem to be worthwhile to me. (I suppose we could look at dynamic auto-linking again, though that isn't a pattern we use anywhere else.)