I have had hives from soy milks made on shared (and thoroughly washed) lines with almond, but my almond threshold is obnoxiously low. If you find that you have to avoid shared lines completely, you may be out of luck. (Shared and thoroughly washed lines with dairy is okay for me, so we use Natura soy milk - they have never had a recall due to dairy, however.) We have had success in making our own soy milk before, although it wasn't quite as good as store bought. Homemade hemp seed milk was easier and tasted better.
For baking, we often opt for using applesauce in place of milk.