The sentence is complicated. I think maybe the best thing to do is re-word the sentence in a way that might be easier to understand.
Jonas and Gabriel saw deer; and once, beside the road, looking at them curious and unafraid, a small reddish-brown creature with a thick tail, whose name Jonas did not know.
Jonas and Gabriel saw deer. Another time, Jonas and Gabriel saw a small reddish-brown creature beside the road, with a thick tail, who was curious and unafraid while looking at Jonas and Gabriel. Jonas did not know its name.
The most ambiguous/confusing part of this quote is that the second clause of the sentence (everything after the semicolon) is incomplete. It's really just a noun (a "creature") surrounded by a lot of modifiers. One would normally assume a noun in an incomplete sentence to be the subject of the sentence, but in this case it is actually the object. The subject ("Jonas and Gabriel") and the verb ("saw") were both left out of the sentence. The only way a reader could figure this out is to understand that the small creature, like a deer, is another animal that Jonas and Gabriel might see.
Another tricky part is here: beside the road, looking at them curious and unafraid. Both phrases describe the small creature, not the humans. That is why "curious and unafraid" are adjectives, not adverbs. The small creature is beside the road, and the small creature is curious and unafraid looking at "them," who are Jonas and Gabriel.
To try to answer your second question, I don't think the deer or small creature are related in any way. In the first half of the sentence, Jonas and Gabriel saw deer; in the second half of the sentence, Jonas and Gabriel saw a small creature.
By the way, I think Lois Lowry is probably a woman, not a man.