Its odd that a normal smoke bomb can block the rinnegan's vision (as seen with Nagato) yet a sharingan can see chakra through solid rock (as seen in Sasuke / Itachi vs Kabuto). And Madara being able to see chakra points makes it seem like rinnegan would have some ability to see through a simple smoke bomb.
Theory: Nagato is never shown looking at chakra points and its said only a original owner of the rinnegan can use rinnegan to its full power. So maybe Nagato can't use the rinnegan's vision ability's as well as Sasuke and Madara can. Sasuke has access to sharingan power with his rinnegan that Nagato doesn't have.
So I wonder if Sasuke could see through a smoke bomb or at least be able to see a persons chakra through the smoke. EMS Sasuke hints he can see in the dark and he can see chakra through rock so why would smoke completely block rinnegan's vision?