If the bottom of the engine mount is flat then you can put a bolt completely through the mount and put a nut on it as you mentioned. If you do use a nut use a thread locking nut to prevent it coming off. Or you can tap the hole as well. Either way will be ok. Another alternative on smaller engines (60 sized and below) would be use sheet metal screws. Drill a small pilot hole and then screw the sheet metal screw in to cut it's own threads.

I had an incident with thread lock and engine mounts before. I used the thread lock and a tapped engine mount and it actually softened the threads to the extent that the mounting bolts pulled out. Thread lock should only be used on metal to metal contact, such as nuts on a bolt.

Hope this helps

Ken