I definitely don't agree with not being able to see Reapers on the map. It's part of the risk/reward. HOWEVER...
As it stands, it is WAY too easy for players to choose the "safest" server to do their voyaging as an Emissary. People switching servers before leaving the dock when they see a Reaper is on the map is the reason portal hopping is justified. People complain about Reapers all the time for various reasons...yet when they're trying to do their emissary ledgers, they'll hop as many servers as they have to in order to find one without a Reaper on it.
Here's my idea. I've suggested it before so I'll just copy/paste it...
-1) Get rid of the little ships on the Reaper emissary table at the outposts.
-2) Crews can only see a Reaper on their map if they are running an Emissary of any kind and are Grade 3 or higher. The logic here is that crews would be invested enough in a server that they'd at least consider continuing with their risk even if they end up seeing a Reaper on their map after they've hit Grade 3. Sure, some people would still immediately sell, lower, and abandon the server, but those are the folks that aren't going to fight anyways. At least with this, their rewards/time would be impacted accordingly.
-3) Grade 5 Reapers can only see ships on their map that are Grade 3 or higher. The logic here is to complement the above rule so that you don't have a tactical advantage on low grade emissaries.
-4) Reapers can only see other Reapers once they've achieved Grade 2 or higher.
All of these things together would make the risk/reward of emissaries on every server way more organic and high stakes.