Should you implement ISA S88 batch controls standards?
Yes. 
When? Any time you automate a batch process or update batch controls.
S88 defines good design and operation practices to improve control of batch manufacturing plants. It is basically a success guide built on the experience (and scars!) of many batch practitioners. Although initial compliance usually requires some extra effort, the benefits of S88 nearly always exceed the time and cost.
S88 is not plug and play
Published in 1995, S88 Part One is in use worldwide for simple and complex batch operations as well as other sequential operations such as burner management. As batch combines continuous and discrete processes, the application of S88 to similar operations that benefit from flexibility is un surprising.
While S88 calls for modularity, this does not mean that any phase will work in every application without modification. Done right, it reduces the integration and modifications required to reuse code and recipes.
In other words, while S88 nearly always provides improvements, it is not magic.
Can you do without S88?
You might forego S88 if: A) you have only one process making one product; B) it runs with consistent results across operators and shifts; C) and with minimal scrap and rework. You might also forego S88 if you run everything in manual and always will. But in other than in these rare circumstances, S88 is strongly recommended.
S88 briefly described
Part one of the S88 standard explains how to:
1. Describe your
process or plant in a physical model
2. Define what you
want to do through batch recipes
3. Implement recipes
using equipment logic
4. Coordinate these
three steps in intelligent and reusable ways
The physical model is comprehensive—it addresses enterprise, site, area, cell and unit modules and concerns. Equipment logic is created in a separate step and coordinates with the recipes through interfaces. Equipment logic and recipes can be created and managed independently.