1. I obviously lack a dive buddy when we are away, what is the standard protocol for going on a dive boat without a buddy? Do you let the dive operation know ahead of time? Do you get paired with the DM or a stranger?
On a boat, it doesn't hurt to let them know in advance. When you call to sign up for a charter trip, and reserve only one spot, you can let them know you are a single / unpaired diver. Some ops will even ask if you reserve a solo spot. You will usually be paired with another non-buddied diver, or perhaps put with a buddy team to make a group of three. It is unlikely to be a problem.
2. I would love to go on some of the trips my LDS organizes, do most trips allows Sig. Others to go? Is there a reduced rate for someone who isn't going to dive?
I can't speak for all shops, but we certainly allow / in fact encourage non-diving SOs to come on our trips. There is a slightly reduced rate (maybe ~$200 on a $1595 all-inclusive Bonaire fee, for example). My wife accompanied me to Roatan and twice to Bonaire as a non-diver, and loved it. She brought her laptop, got a lot of work done, had access to WiFi so she could do email, had her mobile phone so she could do telecons,etc. She brought lots of books. We ate meals together and slept together, but most of the time during the day, and often in the evening, I was diving. We did sight-seeing together (or horseback riding on Roatan) on the last afternoons, once I was in a no-fly interval. She always had a blast and appreciated the quiet and relaxation. She also did some snorkeling on her own, or did some arranged activities as interested her. I use the past tense because, two years ago, she finally decided to get certified and now dives on the trips. But, where I usually try for 4-6 dives a day, she usually goes for 3-4, and then retires to the room or pool while I dive some more.
I just can't go without him, I think it would be unfair and somewhat cruel to go on a tropical trip without him.
Possibly. I asked my wife to join the Caribbean trips because I wanted her to enjoy the laid back atmosphere of the resorts (and she did). She would usually not accompany me on weekend coastal charter trips, although occasionally she would, along with the kids, and use the time to go to the beach or do things with them. She goes on a couple of cruises each year with one or more of our daughters and her sister, that I do not go on - I value the time alone to get things done around the house. It all depends on the dynamic of the relationship.
Still not sure if he would go for this as I'm sure I'd be diving the whole time.
Hmm. That's one for the two of you to work out. What I did tell my wife about going on shops trips, before she was certified, 'I would love to have you go on the trip. I think you will enjoy the environment and the people. But, I will be tied up diving almost all of the day.' That worked well for us. Your results may vary.