Hello. Thank you for contacting the Toolset support.
Based on the information you shared with your initial reply, even if you try to use only WordPress without Toolset, having such amount of posts, custom fields, taxonomies will have possible impact on performance. Please note that Toolset set is still not involved yet.
Having said that, In general, performance obviously affects the site speed when you have number of custom post type setup with the number of taxonomies as well as custom fields.
In other words, it depends also on your server configuration (memory,cashing) as well as number of other factors such as how complex your data structure is.
The key point for you should have in mind is that querying based upon custom fields or taxonomy is slow, an unavoidable consequence of how WordPress database tables are structured. (This being independent of Toolset, which is just built on the core WP structures.) As Toolset follows the WordPress standard to store custom fields for posts, taxonomies and users.
So retrieving posts where they have a custom field or taxonomy matching some value is slow, but retrieving the value of a custom field for a particular post is very fast.
Taxonomies are optimized for querying in a way that custom fields are not, and so don't have the same limitations (and what limitations there are come from WP not from Toolset).
Regarding your another question about "The value column in the custom field table is not indexed":
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That's true, as I already acknowledge that Toolset follows WordPress standard to store custom field. So, for instance custom field value will be saved to postmeta table and where its already mentioned that you can not index the value column and even if you try to index it there will not be any effect.
I suggest you should try to setup a test site and step by step confiture your post types, custom fields and taxonomies and see in action and check what you can do with such big amount of data.