When and how many Colonies are dependent on difficulty.
IIRC successful base defenses might reveal the source (it might even be guaranteed).
IMHO April is really late. It is possible to be allied with everyone and have researched everything by mid March (on Legend).
You don’t need Citadel or Scylla for a faction ending.

In my current Etermes run it is mid February and have ~1 day research time left for the final NJ research. I already faced (and killed) 3 Scyllas.
From my TFTV.log:
[TFTV @ 5/13/2024 2:04:08 PM] PANDORAN CITADEL is 4.253318 from Australia in mist? False with a telepathic captive? False player researched Project Domovoy? False, colonyCounter is 20, multiplier is 1, so adjusted counter per day is 20,and accumulated counter is 100
[TFTV @ 5/13/2024 2:04:08 PM] PANDORAN CITADEL is 2.849063 from China in mist? False with a telepathic captive? False player researched Project Domovoy? False, colonyCounter is 20, multiplier is 1, so adjusted counter per day is 20,and accumulated counter is 217
[TFTV @ 5/13/2024 2:04:08 PM] PANDORAN NEST is 1.612586 from China in mist? False with a telepathic captive? False player researched Project Domovoy? False, colonyCounter is 5, multiplier is 1.387414, so adjusted counter per day is 6,and accumulated counter is 223
[TFTV @ 5/13/2024 2:04:08 PM] Evolution progress is reduced to 35 per day
[TFTV @ 5/13/2024 2:04:08 PM] There are 3 nests, 3 lairs and 2 citadels on 46.00:00:28.8000000

It is on legend, i can go for the anu ending, but i kinda wanna see the Scyllas, they also never showed up on the pandoran evolution report. I wonder if it is a bug, most of the bases are infested at this point so activating them and clearing them to build radars and wait for base defence to get a chance of maybe revealing a citadel seems like a lot of effort that will leave me very dissapointed if it is a bug in the end. :)
Pandoran evolution was also empty for a few rounds until i got some new tech ( Virus sniper ) that made new evolutions possible, maybe i am missing something. Also skiped a month or so to see if the one lair i had would evolve into a citadel, also never happened. :)
So yeah...

Scyllas don’t show up in evolution reports anymore. Not a bug.
Clearing an infested base is actually an easy mission. Go for it just for the XP/SP. Ofc only if it make sense on the Geoscape level.
Anu ending on Legend is doable. On Etermes probably not. You can only deploy 7 soldiers (exception is the more mist but +1 slot VO) but get Taxiarch Nergal + the Exalted.

Can Scyllas only be in missions that are close to a citadel ? Never had a game where they didn´t show up in a random haven defence sooner or later. A scanning drone like the Archelogy ones for detecting colonies would be cool. Ye, i have fun testing builds and stuff, just got a bit concerned that it might be a bug.

My recommendation: forget about Scyllas and do the Anu ending ASAP. To experience more content start another run.