There are several reason why a presenter (of any kind) will comment "Good question."
- The question is good and the speaker wants to provide positive reinforcement for other participants to ask questions (feeding each person's need for praise)
- To give themselves time to think of an answer
- They don't know why, they just do it.
In the case of (3), it is usually taught for the reason (1). That is, speakers are taught to play to the ego or rather give positive reinforcement to the audience which will in turn lead the audience to think more highly of the speaker ("Wow! That speaker really sees how amazingly clever I am."). There is a very real psychological issue going on here and one which is properly used all the time (in and out of the classroom). It is not to patronize, it is to give credit where credit is due. Those who do not know why they do it, can end up patronizing but that is just from a lack of understanding and experience.
The reason is psychological but only partially to make the person asking more receptive to the answer. It is also to encourage others to ask more questions.
Point (2) does happen and it perfectly acceptable. It is not the comment that is the concern. The concern is whether the speaker should know the answer and does not. When I am asked questions for which I need to think for a moment, I will openly say so: "Hmmm, I've never heard that question before, let me think for a moment." If the needed thinking time is too long I will refer the asker to follow up 'offline' so it does not interrupt the overall flow.
In any case, if a presenter is dancing around an issue to avoid showing ignorance shows a lack of confidence which is usually also shown other ways leading to a weaker overall presentation.