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We are just beginning to test some tools to get data out of Marketo into our data warehouse. For that, we are using a third party tool. One of the tables (a Marketo system table) I see created is a "lead" table.
It's not a "table". It's the response from a REST API endpoint. The decision to present it as a relational "table" is entirely up to the consuming application (and often an incorrect use of the RDBMS concept).
Is this table all the contacts (with email/without email/unsubscribed/marketable leads etc) that I have in my Marketo instance?
Depends on the 3rd-party tool and whether that application applies filters to the result set. Most likely, it is indeed supposed to be all People/Leads in your Marketo instance (Marketo doesn't use the word "Contact"; all instances use "Lead" in some places and newer instances use "People" as well).
Again, this is not a table. The REST API does not return tables. It returns JSON-, CSV- and/or PHP-serialized data.
I tried to read the documentation on Leads API but it was difficult for me to follow since we are relatively new to Marketo.
You need to ask the 3rd-party vendor. The filtering (and therefore the count) in a 3rd-party application is entirely under their control. It's likely that they (a) are not reconciling deleted leads and/or (b) did not fetch all the leads from your Marketo instance. It's extremely easy to introduce such discrepancies if the product has not been meticulously designed to avoid them.
Thanks, Sanford! That was really helpful.