Note: this isn't my solution, this is simply my findings from many github issues and blog posts coalesced into a single place.
To fix node-oracledb's reference to Oracle Instant Client on El Capitan, you'll need to run this from any repo that has node-oracledb as a dependency. Lines 16 and 17 need to point to the location of your zip files.
First, you'll need Oracle Instant Client on your machine. Once you click the environment that suits your needs, you'll need to grab two packages: basic, and sdk. Here's an example for the OSX client.
In the bash file also included with this gist, lines 16 and 17 need to be tweaked to point to those zip files you just downloaded.
Once that's done, you'll need to run it from your repo that has node-oracledb as a dependency. So, for example, let's say I had a folder structure like so:
- dev