Well Nanex, to be direct with you, the story is hard to believe but giving you benefit of the doubt, even if there is no certificate of incorporation or MemArt, there should be registration of business name and licence to trade/conduct business from a state or local government agency. This is especially so in Nigeria where there are so many regulations geared towards registering businesses for the purpose of taxation. You can't do business here without TIN - Tax Identification number at one level or the other. So get the relevant registration docs for your boss's business and pray they will be accepted.
Secondly, for somebody who is applying as a Federal Skilled Worked, a professional, to say you are collecting your salary in cash, is also hard to believe. Didn't you say you are a Master's holder? What sort of organization pays a professional in cash, even contract job and you didn't ask questions? Not trying to disparage you but this is how AVO will view your position, it's just too hard to believe. Afterall, you are not a plumber or road side mechanic! You can include a copy of your employment offer letter and highlight the part where it says you will be remunerated with cash. But you can be sure that AVO will verify the authenticity of that claim and the organization (your employer). You are going to face complete and comprehensive background checks. If they can not find any acceptable legal documentation for the existence of that organization, your position won't be good at all.
You can save the day be providing your bank statement nonetheless, showing how you were banking your cash salary after you got it from your employer every month. If your employer was running away from bank trail, at least, it is expected you did the right thing and put your salary in a bank. Nobody will believe a professional was putting their money at home under the bed or are you going to claim that you were using it for another business of your own? if so, hope you declared that business with your initial application! In this age of anti-money laundering regulations and BVN, it only makes sense that you have a bank account where you were keeping the bulk salary money first then making withdrawals for your daily needs or to any other business. Any other story will only be viewed as fairy tales.
Sorry if my response seems blunt, but with the information you provided, this is my humble take based on my experiences and study of AVO and such situations. You may PM me with more details because there is more to this issue than you are saying. All the same, I wish you the best.