2. "He is a very nice guy."
Using a linking verb (i.e. is), you are stating that someone or something has a quality (i.e likeable personality). With your sentence, the reader can imagine that you have known someone for some time, and you are describing his personality.
1. "He happens to be a very nice guy."
The expression "happens to be" implies that, by chance, you notice a certain quality about something or someone. With your sentence, the reader can imagine that perhaps you just had a conversation with a stranger or someone whom you barely know, and he turns out to be amiable.
I hope this helps.