The ability uses 24 hours as a baseline time, which is clearly "1 day and 1 night". The intention behind this is, that the Witch Hunter - as an Inquisitor-like archetype (remember, besides the 3rd Party Fighter Witch Hunter you have, there is the Witch Hunter Inquisitor and Witch Hunter Rage Power and Witch Killer Slayer Archetype) - looks for hints and clues that tell him that a witch was there. These are tiny signs, like making tiny protective gestures or using an evasive speech on some topics. To get these, the inquisitor has to spend time in the community or area.
Shortening the time drastically changes the style how this should be handled:
The Inquisitor picks up the signs as he goes, not really spending too much attention on them but at times spending a moment to reconsider all the things he has seen in the last day to conclude if there are witches (by using the ability). 8 of those 24 hours he will sleep anyway, so spotting something to get those conclusions in 16 hours seems guaranteed. Doing the check to draw a conclusion is the result then.
This still is more or less in tune with the full day, but might be better for the balancing a bit, at least if he spends not most of this time asleep (8 hours of night's sleep make this 4 active hours!) - he should have a chance to actually see those tiny signs! I wouldn't consider it a game breaker though, as I deem 4 active hours fair game too.
Now, this gets more troublesome. 6 hours is not terribly long, not terribly short - a night's sleep is longer. So those should be spent awake. 6 hours awake is like arriving at 6 PM, going to bed at 9 PM, awaking at 5 AM and leaving at 8 AM after breakfast and some talk with the early risers. That is (all in all) a 14 hour stay with night's rest in the mid. It sounds pretty reasonable to familiarize yourself enough with a town in 6 active hours.
4 hours awake are easy to get in a community and allow a decent amount of interaction with the people - arrive at 7PM, go to bed at 10, rise at 6 AM and leave at 7 AM - a 12 hours stay in an inn becomes a perfect opportunity to look for the signs of witchcraft and check for it! With 4 hours of active time, you might manage to become familiar enough, just barely.
Now, here it starts to become unhinging the fluff from the mechanics too much - that is, unless you up the DC. Think about it: go to a different town and try to spot if something there is odd or differently handled from your hometown within the first hour. Clearly, too short how familiar do you become with the people in a bar in one hour? not very.
Now, the ability is described in a way, that implies to me it bases on interaction with people and the place to familiarize yourself with them. How many people can you interact with in 10 minutes? At very best 10, unless you assemble them all in one place and hold a speech, and even then you are not really familiar with any of them.
1 round are 6 seconds. Now you clearly overdo it: Witchhunter arrives in town, takes a look upon the houses and yells "There's a witch in town!" might sound cool, but it is not really fitting the investigative character.