Housekeeping at my MIL's MC seems practically nonexistent. FIL is paying good money for this care, do I speak to someone or butt out?

There’s no doubt I’d mention it

Mention it.
You are paying for a facility to provide a Clean and safe environment. It sounds like neither is happening.

You speak to someone.. ASAP. You are indeed paying good money for care, and a dirty toilet is not good care, and dangerous. Leave out the bit about the smoke breaks,, just stay on topic about her room being dirty and what can be done about it. Take pictures if you want, and talk to the DON about this.MIL deserves better, and so do you.

Yes, mention it to the director/Administrator. Cleaning is part of Moms rent. I had this problem with the Homemaker dusting. I was told they told her not to anymore because some nick nacks were broken. I told the Admintrator I understood but, her headboard was not dusted. The large window ledge was not dusted. (Big enough to put plants) Her TV and a small shelving with only her Bible and box of cards. Her nick nacks were on scarves so the area around them could be dusted.

I may even mention the numerous smoke breaks. They seem to be interfering with her work. The HM is allowed in an 8 hr period two breaks and a lunch break. She can smoke then. I am big on your there for 8 hours, you work 8 hours. Thats what ur paid for. Any less, and you are stealing.

Wow, there is an ALF where you are allowed in to this extent right now? I am surprised. You mention your Mom's place. There is, other than her own rooms, a general living area I am supposing? How do you find that area, the dining area, etc, the communal area to be?
For my bro, he hated the housekeepers visits. He didn't want them in there and he didn't want them dusting his beautiful last collections, the remainders of his pottery collections and etc. He would kind of chase them out if I can put it so bluntly. If you find the over all areas of the facility wanting I would report these findings to administration, with photos if you are able. And I would ask for followup. And I would look into other facilities if they are in the area.
I found the place my brother was in so meticulous about cleanliness. I was absolutely amazed at their housekeeping, their grounds. It CAN be done, but it requires a good management, and the hiring of enough employees. I am assuming that the place you are now judging is not dealing with Covid-19 and the extra hours consumed by same.
Wishing you good luck.

If she's getting paid, youou should deffiently say in a nice way, something about what is lacking and what is expected of her.

Maybr she is paid to just tidy up?

Maybe no one had told her what to do.

Check first to find out what her chores are suppose to be.

Make a List of things that need to be done.

Dont worry about her cigarette breaks as long as she gets done what's on the To Do List.

Since he is paying for the services, administration will most likely need him to complain, Start by asking FIL about the housekeeping services. If he has a contract, look at it. If it is part of the residential services, you can find the details from administration. Then, document what you are seeing: pictures, dates, times.... Give FIL copies of your documentation and explain your concerns. Offer to go with him to administration to talk about your concerns.

If you are going to speak up, then take pics (with time stamp) and document the absence of cleaning. A certain amount of "supplemental" cleaning is fine, but if there are serious signs of chronic lack of cleaning, it should be brought to the attention of management. When each of my parents required LTC, I found myself cleaning surfaces regularly.

If the cleaning isn't being done, I would worry that the safety protocols surrounding CoVId would also be sub par.

I would say something. You can be assertive without being aggressive.

I would be sure to assess the overall situation before "picking my battles". Where my mother was, various things, such as the opening of the venetian blinds, the switch for the light over the bed, etc. didn't work properly which were direct inconveniences. I never got around to noticing whether there was dust. The place was run about as well as a university dormitory.