Yes, but why should there be a concern about the number of table rows. Both the meta_key and the meta_value are indexed columns and the number of rows in the database will have negligible effect on the query time. And it also seems that you’re example is a bit extreme, 30 checkbox fields associated with a single post with 15 values each.
If you were not using ACF and you constructed you’re meta fields yourself and stored them yourself, this is the same way that the values should be stored if you want to be able to easily search those fields, this is how WP works. Is the situation ideal? Probably not, but if you choose to use WP then you need to function withing the boundaries that it sets.
