public class dialog
    {
        public virtual ICollection<users> members { get; set; }

        public virtual ICollection<users> readers { get; set; }
    }

    public class user
    {
        public virtual ICollection<dialog> membersOf { get; set; }

        public virtual ICollection<dialog> readersOf { get; set; }
    }

    user user = getUser();

var new_dialogs = user.membersOf .Where(x => !x.is_deleted).Where(x => !x.readersOf .Select(z => z.userID).Contains(user.id)).Count();

var new_dialogs = dbContext.users.Select(x => x.id == <ID юзера>).SelectMany(x => x.membersOf).Where(x => !x.is_deleted).Where(x => !x.readersOf .Select(z => z.userID).Contains(user.id)).Count();