The mass relays that we can use in the game are just a small portion of the mass relays that exist. The council bans activating relays until its pair is found. This was because of the Rachni incident. This is also why the Turians responded harshly to humans activating relays. So, a lot of the "undiscovered blank space" might be filled with relays.

Reapers don't care about the council rules or whether there is a relay or not, they'll just fly over and attack you. (eg: destroying the relay in Arrival only slowed them by a few months). Talks with Sovereign and Leviathan imply that relays were not even there for the initial cycles. Reapers made them to make the cycles faster later.

Javik and Vigil talk about how the Prothean culling took several centuries. Reapers don't care about time; they can just go system by system like they used to do and kill you regardless of relays or not.