They pay by the system so if, for example you find a system with 8 landable life-bearing planets each with 8 different species it's still just one entry on the data page. 3 pages of systems is potentially a huge amount of samples or possibly not that many depending on your system to planet to life signs ratios.
Some clarifications here:
It lists the bulk payouts by system, but, if you sell each system individually it shows you all the planets and their flora rewards. Rewards are paid out by each flora scanned, duplicate flora on separate planets in the same system will both payout appropriately for first footfalls etc.
The bonus 100% rewards
do not count towards your Elite Ranking. First footfalls are meaningless for your rank which means It is likely that someone in the future will develop a "Road for Exobiology" with a list of 100ish planets and their flora coordinates in and around the Bubble that anyone could just follow to complete their Exobiology grind if so inclined. I
suspect this mismatch in payout vs expected rank boost may be creating an illusion of lost data BUT...
I too noticed data 'felt' missing and started paying more attention to what I was selling and noticed 2 bugs that suggest lost data may be a thing (but in no way prove it just something along the lines of where there's smoke...)
Bug 1: You can sell all pages of your data, leave the window, talk to the npc again and often times there's another page of data that magically appears, and
Bug 2: If you sell a page of data and click 'Next Page' your game crashes.
That said, when I sold systems individually later on in my Exo-mightiness career it 'seemed' correct (I didn't take meticulous record of exactly where and what but did see appropriate amounts of low value systems vs Water Atmo worlds which was a behaviour I changed as part of this test). This could either be because patch 6 shadowfixed an underlying server issue that was corrupting Exo data or that data only starts getting lost if you have a LOT of data (5 pages or something).
My personal belief is that this is simply your subconcious telling you this is not worth it. You literally spend months out in the black landing on god knows how many planets, endlessly searching for the same stupid life blocks only to return to 3 pages of data that sells for half a mining load? Cognitive Dissonance is a b