How do you know that the farm cottages had any dogs? If they did maybe they were asleep inside anyway, out to the world!
Once he approached the cottages and WHF entrance what was to stop him dismounting and walking with the bike?
If the guard dog was kept in one of the outbuildings/barns as has sometimes been stated how on earth could it have heard anything on the opposite side of the house where JB got in? Particularly if he left the bike near to the entrance gate and crept up to the window out of sight of the outbuildings.
Jeremy Bamber was familiar with both dogs (and they with him) working at the farm during the day, having meals there and using the office. If any of the dogs slept in the woven dog bed in the kitchen they would have recognised him as soon as they saw and/or scented him, giving JB enough time to pacify them should they have started to bark.
Many dogs tend to sleep overnight. My mother's dogs bark out the windows or by the front door at every car that goes by. Just hearing a car is enough to make them bark. They also bark if they see people walk by. At night they are tired and don't do this.
I went to my parents' very early the day before Easter to set up the table for Easter. I had to bring 8 extra chairs and put 2 leaves in the table. The dogs did not bark at my car nor did they bark at me before recognizing me. When they eventually came downstairs to see what the noises were they didn't bark they simply wagged their tails and greeted me then laid down to rest some more. I don't know if they were awake or not when I arrived.
Dogs tend to bark moreso during the day and at people they don't recognize.
As you pointed out they could have been sleeping, could have been far away from where he entered and also since they know him they would be unlikely to bark at him if they did encounter him.
There is no reason ast all why the fact they had dogs would scare him from trying to kill them. The only thing that would keep him from doing so is his conscience. The notion that he would be too scared to try because dogs might tip them off that he was there is absurd.
Evne if tipped off they know him so would not be overly worried but they would have found him armed anyway and he could simply shoot them then.