Performance basics? BlogPost+Comments vs. One ever-expanding Matrix Field?
Regarding performance:
If you look at the database structure of Craft, you'll see that Matrix content is stored across multiple tables, with each block having its own record, just like entries do. I've never compared calculations, but I'd bet there's no significant difference in the DB performance between your two ideas. Using eager loading you could retrieve a BlogPost entry and all Comment entries related to it in three DB queries.
If you want to run a quick exercise to test your theory of performance, model out both options. Create one entry that has 10 &quot;comment&quot; Matrix blocks, and one entry that has 10 related &quot;comment&quot; entries. Don't even worry about a front end, just create two empty templates—one for each approach—that get the respective entry and its comments. Use the Yii front-end profiler (activated under your user account's Preferences tab) to check out the performance difference. This will suggest what kind of performance difference there might be.
Also keep in mind that once you layer on your page caching strategy, performance differences might be a moot point.
Regarding usability:
From a management standpoint, idea 1 sounds much easier to work with, as you're utilizing Craft's content structure in a natural way (as you said, idea 1 is a well-tested and proven approach to this use case). Craft already exposes a very streamlined API for creating, editing, deleting, and querying entries. Doing the same for a Matrix field on an entry is certainly possible, but you'll probably end up writing your own interface if you plan on doing that at scale.
Also consider the interface within Craft for you to manage things. A Comment entry type already has a dedicated admin section for you to browse, search, sort, and manage comments. Trying to do any sort of query across Matrix blocks distributed among BlogPost entries is not built in to Craft's interface; you'd have to write a whole plugin to add that functionality yourself.
I'd go with idea 1 for sure.