As per my experience, indexing can cause issues with the SAP database performance, Hence, indexing reorganization may be required in SAP. We did it in previous implementation.
We faced with indexing problem with one of the big SAP table. The indexing created by us was causing conflicts with the indexing provided by SAP. The search on the table was very Slooooow. As only selective transactions ( related to material documents) were effected, it was obviously not server issue.
We reorganized the index and everything was OK after that.
I suggest, you may check the traces on few key heavy duty tables in SAP. This may help you to find if there was some conflict with the indexing on that field.