Not a dumb question at all and I think I see where you are heading. Basically you are asking if you apply an antimicrobial that causes a 99.9% reduction and then apply the same thing again how many are left? Or, how much additional killing do I get with the second application. This is actually a complicated question and it raises a number of factors I left out of the original article for the sake of simplicity. First, the manufacturer’s of antimicrobials are often times pretty cagey about what they mean by 99.9% or whatever % effective. There are a number of different ways to do the experiments to generate the data to make these claims and there are many variables one can tweak to get the desired result. First, the selection of microorganisms one tests the antimicrobial against can obviously have a big impact on the results. Some are more resistant to different antimicrobials than others. In general the major manufacturers test against a suite of common bacteria and viruses that are well characterized but in the real world this is not the case. Also, the way the microbes are grown and where/how they are exposed to the antimicrobial influences the results in a very big way. In nature microbes, specifically bacteria almost always grow in what are called biofilms. These are basically large groups of bacteria (millions upon millions of different species) that all clump together and exude and extracellular polysachharide matrix that protects them from harm in the environment including antimicrobials. They do not grow alone or even in groups of all the same species. Antimicrobial testing is rarely performed using bacteria in biofilms as this is a much more difficult and expensive thing to do practically in the lab. Also, one needs to remember just how small micro-organisms are. A toilet seat may look like a smooth surface but to a microbe it may as well be made up of a series of Grand Canyons and mount Everests. I exaggerate some but not by a lot when I say that. There are many, many, many nooks and crannies within which any given microbe or more typically biofilm can “hide” and shield itself from exposure to any given antimicrobial spray or gel or whatever.
But ignoring all those complications to answer your question let’s look at the 5 million example again. You hit it with an antimicrobial that is 99.9% effective and are left with 5000 remaining. Now you hit the 5000 again with the same antimicrobial and you are left with? Just do the math again 5000 x 0.999 = 4995. 5000–4995 = 5 bacteria remaining. Sounds good, and it is but again remember for some bacteria the infectious dose is as low as 1 organism. You would have to hit those 5 one more time with the same spray to get to less than one remaining (0.5 to be exact). Of course because of all the complications I mentioned above it doesn’t work like that in the real world and in general as microbial populations get smaller they get harder and harder to completely eradicate. It is a probability game really. In order for an antimicrobial to kill a bacteria it needs to “find” it, and the less there are the harder they are to find. Laboratory testing of the kind used to generate %effectiveness claims ignores all of these real world complications and is therefore even more deceptive than the math alone suggests.
Btw I commend your hesitance to use antimicrobials willy nilly. Antimicrobial resistance is a real problem however in the case of common household cleaners and such resistance is not really an issue. This is only really a concern for antibiotics which kill microbes in very different ways than things like alcohols and bleach. It is still good to resist the urge to over treat with any antimicrobial because by and large the vast, vast, vast majority of microorganisms are extremely beneficial and we could not live on this planet without them. There is a strong argument to be made that overuse of antimicrobials “clears the playing field” of these good microbes which typically crowd out the few pathogens thus actually exacerbating the problem rather than making it better.
See this article I wrote a long while back for more.