About 1/4 million per year - that's how many people are missing (20 year average) according to http://www.scoop.co.nz/stories/WO1308/S00441/4432880-missing-persons-vanished-in-past-20-years.htm
If you increase it gradually enough, I think pretty much any number - we get used to things pretty quickly.
If you kept it under (remaining population)/(Dunbar's number) per decade, and had it evenly distributed, then most people would know about 1 person missing per decade - not enough to raise suspicion. Dunbar's number is a "suggested cognitive limit to the number of people with whom one can maintain stable social relationships" (from Wikipedia), and varies, but is usually considered to be about 150. This comes out at about 45 million. As I mentioned, you'd need to ramp up to this gradually.
Depending on how much intel you have, you could increase this substantially - anyone who has not spend X hours with other people in the last month; wars are pick & mix; anyone out at sea; in storms/floods/earthquakes. Any situation where personal communication is down for a period. Grab the odd plane; mountain climbers etc.; people with depression. Or, induce depression first, wait a while, then grab them.
Monitor mass media carefully, if there are any reports, stay at that level for a while - people will get bored of the news if it comes up regularly.
If you can replace them with fake corpses, it's even easier. Replace a pile of prostitutes with fake corpses (optionally framing someone), wait for the news story to hit, then start introducing "copycat killings" - wait for that to hit, repeat, repeat, repeat. Gradually generalize who gets killed - start with someone cliche (prostitute), then each "copycat" takes a different aspect from the newspaper - one "copycat" may target women, another the clientele of the prostitute, a third poor people; in the next generation, women becomes professional women, clientele becomes men in general, poor people killings are "copied" as African-American (implying a racist element). Each subsequent "copycat" takes one element from the mass media reporting, and so over time mutates the target.