The general convention about this question is to run each Shopify store on a separate pixel. But technically that's not necessary. You CAN run multiple stores on the same Facebook Pixel.

However, you should be aware that Facebook reports give no indication as to WHERE a conversion happened. Even in the same store, sales could come from a different product than the one that is targeted with any specific ad.

This is also true for different stores that use the same pixels. So you should keep that in mind when you decide on your pixel setup for multiple Shopify stores.