I’m sure that MikroTik can easily write their own ACME client. But it’s even more important how it should fit into RouterOS and work for as many scenarios as possible.
For example, maybe you just want certificate for https WebFig (or SSTP server). Sounds easy, right? There’s already a webserver on router, so simple http-01 validation can be used. But what if you don’t want or can’t open port 80 (AFAIK http-01 always starts with plain http on standard port 80)? It would be the case on at least half of routers where I’d like to use Let’s Encrypt certificates, because there’s typically only one public address and standard http(s) ports are already forwarded to some internal webserver. There would have to be support for dns-01 validation and it has different problems too.
I think it’s doable, I tried some suggestions in Support for ACME/Let’s Encrypt certificate management thread, but so far it doesn’t look like anyone from MikroTik though “oh yes, it’s super-awesome, we need to have that!” Maybe try to invent some other foolproof plan that will finally convince them.