Should guild members focus on fighting the Guild Bots, their own Bots, or does it not matter? Does any strategy earn more or less points for the Guild?
That tactic is trash. Higher bots give more points so if someone goes waaaaaaaaaaaay higher, then leaves some bots to be attacked (or rather, tap fight and retreat) for every other guildmate, the amount of points gotten is much higher.
Yes, encourage everyone to hit one guild bot only. You get more points for higher bot level, more points for the guild bot than your own, and it can be hit by anyone at any time.