Depends on what google photos you are talking about. If you are talking the different photo apps on the phone itself, then yes they are looking at the exact same files. So if you delete them through one app, then they are deleted on the device. Meaning no app can see them anymore.
If, however, you are talking photos you uploaded to or synced to a google account, then that is different. When deleted on the device they should still be on the account. Unless you have the sync set to update regularly and then it may see that it is gone on the device and delete it on the account.