Zen : Dilithium Exchange
Currently it has already begun the slow drop in the value of zen to dilithium. This is a day after a new 5,000 zen ship pack was released and a very bad sign. While it is true that they are returning the Dilithium to STFs I highly doubt anyone will argue that the supply of dilithium has gone down and that demand will increase. And while Zen becoming cheaper is good for me, it is bad for cryptic. I would imagine that as the value drops so will the traded volume as both sides believe their currency is being undervalued on the exchange.
Lock Box/Master Key
Even with the highly desirable Reputation Mark Boost and mirror escorts that we all know will be in the next lockbox I would expect the sale of Keys to drop significantly. There will be three main factors that cause said effect. The first being general consumer fatigue, those that would buy 200 keys for a ship have likely been burned enough times by now that they have learned. Not all but many. Secondly many people (myself) only buy lockbox keys with zen I buy with dilithium and as I said before I expect the volume traded to decrease. And finally with the redesign of the STF loot system they have chased away the player's who really enjoy the rush of the random loot drop. I would guess that style of gamer would be more likely to partake in the lockbox system than those who enjoy a predictable grind.
Because of the doff changes combined with the removal of the console clickers many fleets will be hard pressed to accumulate the resources need to advance their fleet along with the new reputation grind and embassy. I suspect many will try and get their embassy to tier 1 if they can stomach the dilithium costs and then abandon it. I also suspect many fleets have stalled in their starbase progress to begin with and that many many more will as well.
TLDR: Many changes have been made that will cost Cryptic revenue IMHO.