That is a possibility, yes. But... You could say the same about running high I/O dev/test on the same filers as production, whether they are clones or not. Some things to consider:
1. If you are running dev/test on the same aggregate as production, the disk load will be shared whether you have flexclones or not.
2. All data on the controller uses the same NVRAM/CPU/ETC. So, FlexClone or not, you are sharing resources anyway.
3. If this is of concern, consider cloning from a snapmirror destination or a DataGuard copy (if using Oracle with DG) on a different filer.
4. Use FlashCache - the shared blocks used in the clone are more likely to be in the cache (as you have multiple clients accessing the same blocks), and will reduce disk load.
Ultimately, it can be a trade-off between the benefits/savings from FlexClone and the cost of dedicated disks/filers/etc. We are using clones of Oracle DB's on some Prod filers, and it was also a concern at the design stage. We took a shot at it and it's working OK 1 year on. Any critical DB's with high IO (such as data warehouse applications) are cloned at DR from the mirrors.
Regards,
Craig