I was using an Asus Zenfone 3 and the manual mode was pretty good. After using it for two years I want to try a Canon EOS M100. But will it be a good option? I chose it because it seems to be easily portable, pictures taken by it are also pretty crisp according to what I saw on youtube and other review pages. But the low light photography reviews are not so good. This raised a question in my mind: can I use other lenses to improve the low light performance of the Canon EOS M100? If yes, then what are the options available? As mirrorless camera lenses are very costly, can I use third-party lenses?
The M100 looks like a good camera the picture quality should be excelent and I would not worry about low light performance, the lenses will have a greater inpact here. According to me the main dissadvantages of the M100 is the lack of a flash hotshoe and a viewfinder. No hotshoe means not being able to attach an external flash on top of the camera and viewfinders are very usefull to both stabilise the camera (by holding it to your eye generating another contact point) and to take photos in bright light where the sun might overpower the screen. An alternativ camera that solves these is the canon m50, the downside of that is that it is more expensive.
I'm not a mirrorless shooter, so take my opinion with a grain of salt... I would go with a Refurbished Canon Rebel T6 Kit. (Which is a DSLR, not a mirrorless camera) I have purchased 5 copies of the previous model in this series (the T5) for my photography students, and they are great. It performs well at high ISOs (which is what you need for low light photography). It's a great way to learn manual exposure and other techniques.
Yes, several other manufacturers make 3rd party EF-M mount lenses. Here are a few. (But keep in mind that they are not always cheaper or better than those by Canon) The thing to look for to optimize low light photography is a lens with the largest maximum aperture you can afford. This allows you to use a lower ISO, and therefore get higher quality photos. (Note that there are lots of other considerations when choosing a lens, such as sharpness, focal length, autofocus speed, etc...) I would do a web search for the name of the lens you are considering and "review" to get opinions on a specific model.
The EOS M100 main advantage is that the mirrorless design means it is very compact and small. Other than the light weight small size you will not improve your photos compared to getting a regular DSLR which you could probably pick up for less.
The other issue is accessories - there are a limited range of lens and accessories. You can use regular Canon compatible lenses with an adaptor though which adds a bit to the size and weight but still lighter than a full dslr. https://www.canon.co.uk/lenses/mount-adapter-ef-eos-m-lens/
I was using an Asus Zenfone 3 and the manual mode was pretty good. After using it for two years I want to try a Canon EOS M100. But will it be a good option?
It will be better (than your phone). But it will not be good by any reasonable measure of "good".
M100 lacks viewfinder. As already explained, it lacks a hotshoe too. The ergonomics look very problematic. About the only benefit for low-light photography that I can see is that the EOS M system has a 22mm f/2 lens for situations where fast aperture is more important than image stabilization. In comparison, the EF-S system of Canon's cheap crop sensor DSLRs lack a fast normal prime (unless you include third-party lenses, or unless you consider f/2.8 crop lens "fast"). However, this is a crop factor 1.6x camera so when comparing it to full frame cameras the f/2 is more like f/3.2 equivalent. Not so good anymore.
It's hard to recommend another Canon mirrorless camera than EOS RP for beginners -- it has viewfinder, good ergonomics for those whose hands are not especially large, hotshoe, and a very wide variety of compatible lenses for a system that isn't likely to die away. The EOS M system is more likely to die away than the EOS R system. Unfortunately, the EOS RP as a full frame camera has more expensive lenses, and as a full frame camera the body might be outside a beginner's budget.
Someday, Canon might release a crop sensor RF mount camera. Before that day comes, you should probably be looking at Sony crop sensor mirrorless cameras.