I'm a relative noob myself, but the way I understand things:
1. They are the same as far as I know
2. Yes, some mods add database tables or columns, but some don't.
3. Yes, having your site dependent on mods can cause update issues. Obviously going from version 3 to version 4 will cause more problems than a version 3 upgrade.
I'm sure someone will correct me if I'm wrong...
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