1. Make cookies: Put chopped chocolates and butter in a medium metal bowl and set bowl over a pan of simmering water. Cook, stirring, until melted, then remove from heat and let cool slightly.
2. Whisk eggs, sugar, espresso powder, and vanilla into chocolate mixture. In another bowl, stir together flour, baking powder, and salt. Stir into chocolate mixture until evenly mixed, then stir in chocolate chips and pecans. Wrap dough airtight and chill until firm enough to hold its shape, 50 to 60 minutes.
3. Meanwhile, make ganache: Put chopped chocolate and cream in a medium metal bowl and set bowl over a pan of simmering water. Cook, stirring, until melted, then let cool. Cover and chill, stirring occasionally, until firm enough to spread, about 1 3/4 hours and up to 2 days. If ganache becomes too firm to spread, transfer to a microwave-safe bowl and microwave for a few seconds to soften, then stir.
4. Preheat oven to 350°. Line 2 large baking sheets with parchment paper. Scoop 2-tbsp. portions of dough onto sheets, spaced about 1 in. apart. Press dough to flatten into even 1/2-in.-thick rounds. Bake until cookies no longer look wet and you can feel a slight crust on top, about 10 minutes (don’t overbake); switch position of baking sheets halfway through. Let cookies cool on sheets on racks.
5. Generously spread flat sides of half of cookies with ganache and top with remaining cookies. (You may have a little leftover ganache.)
Make ahead: Chill filled cookies airtight up to 2 days, or freeze. Serve at room temperature.