Many times thermal pads are used because the gap between the heat spreader and the part is not consistent or even enough to use paste. When you look at GPU heat spreaders they frequently use thermal pads instead of paste for things like chokes and VRMs because they need to cover several of them and can't guarantee a consistent height from part to part. It's much simpler to use a thicker compressible pad to ensure everything has good contact.
Could upgrading to higher quality pads help? maybe. Pads are relatively cheap so it doesn't make a lot of sense that Sony would cheap out on pads to cut cost on a piece of critical cooling structure. You'd be further ahead cleaning dust out and making sure it has plenty of airflow.
If you mean the spots that don't have any cooler on top of them then I would say no,paste is made to conduct the heat to the heat spreader, I doubt it will do anything worthwhile on its own.
Many times thermal pads are used because the gap between the heat spreader and the part is not consistent or even enough to use paste. When you look at GPU heat spreaders they frequently use thermal pads instead of paste for things like chokes and VRMs because they need to cover several of them and can't guarantee a consistent height from part to part. It's much simpler to use a thicker compressible pad to ensure everything has good contact.
Could upgrading to higher quality pads help? maybe. Pads are relatively cheap so it doesn't make a lot of sense that Sony would cheap out on pads to cut cost on a piece of critical cooling structure. You'd be further ahead cleaning dust out and making sure it has plenty of airflow.
You could also go crazy and water cool the thing. Will it give you better FPS...no. But it could be a fun and challenging project.