If I create a binary that contains exactly the same class-, method- and field signatures as a proprietary application, but I've left everything else out - does the license of the original app still apply?
If you take a software binary B, distributed under licence L, and use a piece of software to modify that binary according to certain pre-defined rules, you have created a modified binary B', which is very likely a derivative work of B in copyright terms. The licence on B' will therefore depend on the terms of L.
If L was a permissive free software licence, then although there may be certain labelling requirements for B', it may also be possible to distribute B' under other licence terms, including copyleft and proprietary ones.
If L was a proprietary licence, you likely have no right to do what you've done and are already in violation; see as a random example this proprietary licence, which says
You shall not alter, disassemble, decompile, reverse-engineer, adapt, translate or modify the Software or any portion thereof ... You shall not copy the Software.
I asked at the top how you created this stripped-down derivative work, and you asked whether it mattered. The short answer is that I'm not a programmer, and in any case there are more things in heaven and earth than are dreamed of in my philosophy; so instead of guessing what you'd done and basing my answer on a guess, it seemed simplest to ask for more detail.