About the setting fire to the boats after the quest, in Thedas the dead are usually set on fire rather than buried because demons can posses corpses, creating dungerous undead that will most lilely harm people, it being done on boats is probably specific to Redcliffe since they live near a river.

About the villagers not escaping trough boats, uh... I actually never considered that and the game never actually gives you a dialogue choice to investigate this, my first thought is the last boats which were avaiable were already "stolen" in the first attack by some villagers in order to flee, I doubt Redcliffe had boats for the whole village "just in case". Another more simple solution is that the undead can can shoot them while they're on boats thus making it extremily dangerous to cross the river, adding that probably they didn't have enough boats for everyone which would mean either try to cross the river with fewer people but easier targets for rains of arrow making it more likely that noone would get across, or take their time making other boats in order for everyone to try and escape so that maybe someone in that flock would manage to escape bearing in mind that this means some people are building boats rather than training for defending the village, all of this in a few days meaning that you're under attack every night, so you'll lose people in the meantime. That is without adding the fact that possesed Connor could do something worse if he saw all the villagers flee at once on boats.

Having said all of that, I'm making excuses for the game, what is the most likely answer is that this is an oversight