I had a similar type of wedding, the registry office and hotel where we were having the meal could only cope with 44 so that is what we had - we both have large families, so that was really parents, brother sisters & kids with a couple of really close friends as well. In the evening, we had a buffet and disco at another venue for another 100. This was mainly friends, and less close relatives with a few colleagues thrown in. I have loads of Aunties, Uncles and cousins, so I asked my parents what they thought and at first they were happy not to invite any, they then changed their mind and we invited just aunties and uncles and no cousins as this would go beyond our budget. As far as I am aware, no-one was offended and they all still speak. I am not close to any cousins, so it may have been different then.
I would go with what you want - it is your wedding and your party - I checked with my parents as they did give us some money towards the wedding and as it was the first family wedding for a few years, it was not as if there was a "family protocol" to follow.
Hope you enjoy your day.