Are there such a thing as "junk miles"? Yes and no.
From my own experience as a distance runner, I can tell you that it's all about HOW you accrue your miles, relative to your goals.
If you want to maintain general heart health and wellness, then no, no mile is a junk mile, everything you do is helping you on your way.
If you want to get stronger though, there are obviously some things that are more effective than others. If you want to build muscle and tone, better to pump hard over long distance and go anaerobic. Going two hours at a pleasant 140 bpm will probably not build muscle, unless your max is 160...(I said probably not, everyone is different though)
Personally, whether it's biking or running, I set a lofty distance goal and try to get to it faster than I did yesterday. It's getting harder and harder to break my own records, but I consider it a good workout as long as I'm dripping, regardless of whether my average hr is 170 or 182.