In Deus Ex:HR DC, can I end the suffering of the Hyron test subject and keep the pacifist achievement

Yes it does count as killing people, according to the sources I have read because you created the death indirectly by your own hand.

The related note you mentioned: If the man you walk up to laying on the ground has a Zzz its a knock-out icon. If he has a skull its a death icon. The environment will always tell you these things. If the roof is such a far drop that you cannot ID him, assume you killed him.

If you kill people from range you are potentially missing out on XP, because:

Neutralize an enemy: 10XP
Hand-to-hand takedown: 20XP
Non-lethal: 20XP
Headshot: 10XP

So a non-lethal hand-to-hand takedown is worth 50XP, where just shooting someone is only worth 10XP (or 20XP if it was a headshot) and a lethal hand-to-hand takedown is 30XP.

However, playing non-lethal is more difficult as enemies can be revived and traq darts are slow to act (so non-lethal at range needs careful planning), and only using hand-to-hand takedowns means you're more likely to be spotted or trip an alarm.

Remember that you can get the Ghost (500XP) and Smooth Operator (250XP) bonuses for completing objectives undetected and without alarms (respectively), and I imagine they're usually worth more than the few XP lost by not taking down everyone hand-to-hand, so do whatever you need to do to avoid being detected whenever possible.

You might find What actions give XP in Deus Ex: Human Revolution? helpful.