CyanogenMod's theme engine CMTE was one of the first theming options for custom Android ROMs, but its absence thus far in the world of Nougat and recent chats with LineageOS team members seem to indicate that the popular theme solution is no more and that the popular Substratum theming solution will likely take its place. While nothing has been said officially as of yet, excerpts from a conversation between the lead developer of Substratum and a LineageOS team member indicate that the head of the CyanogenMod Theme Engine project has "moved on," which likely means that we won't be seeing the venerable theming solution again. Given the identities of the chat participants, it is quite plausible that Substratum may show up in LineageOS, especially considering its popularity.
The source of this info is a conversation between Sykopompos, the lead developer of Substratum, and Kover, one of the top developers of LineageOS. When Sykopompos asked about the status of CMTE directly, Kover indicated that "Clark has moved on." The Substratum is based on the overlay framework that Sony uses for their devices. Since a part of this framework is built into the overarching AOSP code for Android, the solution is almost universally compatible and is very easy to implement in custom ROMs. The solution is also modular in nature and allows individual theming of different elements, which is one of the main reasons for its popularity.
Even back in the Marshmallow days, the decline of the CyanogenMod Theme Engine was seemingly coming. BitSyko's Layers, the predecessor to Substratum, was touted as being more flexible and easy to use than the CyanogenMod Theme Engine and found its way into many custom ROMs, especially those that were based on AOSP, rather than being an offshoot of a CyanogenMod port of any given device. Layers' popularity was short-lived, however, as Substratum replaced it almost immediately upon being developed, and most Nougat ROMs do not support Layers out of the box. While Google has yet to build a theming solution into AOSP, the Sony backend that Substratum uses is pretty close, and its compatibility and ease of use have seen it skyrocket to a prominent place in the custom ROM world.