It can happen that you Blood Tap and DS with an unpaired Death Rune and at some point look at at the scenario you described. To illustrate:
Since the game will not prioritize a Blood Tap'd Death Rune over normal DD or FU pairs you will sit on that Rune after the Death Runes at 3 secs are used for a DS.
But this situation can only happen once during one Blood Tap if you put the 2nd Blood Rune on CD before BTing. Now your point is that doing so puts the Death Rune on a longer CD than it needs to, which is correct. But if you let the the first Blood Rune fully cool down and then BT you will usually bug out your Runes (atleast that's what happens to me - might be addon related, not sure): not only do you get a Blood Rune converted to Death Rune but it also refreshes another random other Rune. And whenever that happens to me the game blocks me from doing anything for a while. Assuming that bug is fixed (or that it just affects me for some reason), I am not sure if your method is better - it's worth considering atleast. If there is a way to keep up Blade Barrier and still be able to RE without proccing a useless Blood Rune, that is. I just do it the other way because getting the top 3 D Runes on CD gives you 3 chances to proc RE and keeps up Blade Barrier much more easily.
As for your other questions:
Bone Shield vs half a Death Strike depends obviously. If you don't need to save the BS for a specific boss ability, you aren't exactly wasting it if your lone Death Rune is not doing anything.
HS vs BB: HS is always better than BB on single target. It should do nearly triple the damage of BB in 359 epic gear and you will still want to HS early in a pull for threat. Use BB for the debuff and only if you want to ensure that your Blade Barrier stays up.