My research, let me show you it: http://i.imgur.com/FrzzD.jpg

Well, I have heard this before, but instinct always said something different. Thus science to the rescue: http://i.imgur.com/2EqJY.jpg

Draw your own conclusions or, better yet, test some and share your findings.

Well, I was soloing (which may mean less crowns) so I couldn't catch every single little lichen before it merged... But none of them ever reached spike stage. Still, the difference is clearly minimal, might as well merge or not merge.

It takes 4 to get the to the spike stage so yeah; if you ever want to test it properly (since i won't; no elevator pass) you can use a fixed spawn level (aurora isles come to mind only atm).

Each, smallest lichen has a chance to drop a gold coin. I think i only saw once a the biggest colony to drop two gold coins.
Also, like i said, if you want me to take you seriously you gotta test it in levels with fixed spawns, Lichenous Lairs are different every run and the amount of enemies on them can vary, so can vary the amount of lichens on the arena in the mission. There is too many factors to take in so you can't really claim what you said.

I always let them merge.

Run 1 - 3062cr
Run 2 - 2977cr
Run 3 - 3221cr
Run 4 - 3329cr
Run 5 - 2776cr
Run 6 - 2732cr
Run 7 - 3503cr
Run 8 - 2661cr
Run 9 - 3254cr
Run 10 - 2756cr

I said that no lichen ever even reached the spike stage, as opposed to having large claw lichen that take like 10 or more standard lichen to make. Thus I'd say it's different enough to be admissible as evidence.

And to repeat: Of course it's not real science, that would take 100's or 1000's of runs to account for the randomness. Still, if despite the randomness the results are so close some conclusions can be reached. That's it.

http://sadpanda.us/images/858273-EGIH5AR.png
http://sadpanda.us/images/856001-E9448J0.png
sadly, i must've hit F11 when i went on that 3610 crowns run as i can't find the screenshot and not letting them merge is the only thing that i've been doing

Combuster / Acheron / Barbarous Thorn Blade / Ash of Agni, Skolver set + Swiftstrike Buckler + 1x Elite Slash Module + 1x Quick Strike Module
I'm getting max Damage and ultra ASI with this setup, when i solo, i can twoshot the smallest lichens even at the arena

Wait, so you DON'T want lichens to merge? I always thought you got more profit from letting them merge to the Giant Colony....

Those seems to give much more profit than others. Rise or Fall as pointed out, but Time Enough At Last is fine too (2.9-3.1k average). JK mission is also a good way to farm Jelly Gems, even though it has less payouts.

Now if they released an FSC mission...

For missions, I believe that the RJP is the best place to get money. Don't go saying "But the arena gave me 3K!"
Just do Depth 14 & 15, skip the boss, and you should have around 2200 crowns.
If you have the elevator pass, then yeah it is probably better to do the arena.

"Which is better? Who really cares, since I can get more in FSC, or T3 arenas"
The difference is that there is no FSC mission, so you rely either on luck when joining random parties or on your guildies/friends or you suck it up and go from Emberlight, meanwhile, you can do the mission any time you want.
"better mats."
This is simply not true, ghost bells (good luck getting a drop of one) aside, all the other materials are junk that everyone has tons and doesn't sell , even mugs of misery fall down to as much as 400 crowns.

Its all about efficiency - want to have the fastest crown gain without having to rely on anything? The arena mission is the obvious choice, do it, back to haven, drop off warp dusts/bushy tails/drake scales/monster bones/green shards in AH and do it again.