Definitely take the sill covers off and put something inside.. but NOT undersealing/waxoyl, please. That might fill the sill cavity and make you feel safe but you're missing the point of the sills, which are not a regular car cavity...
If you spray WAX inside it'll stop the drain holes from draining. Those holes need to be kept open so that they can let water out if any gets in, and get in it will, the soft top draining system isn't perfect..
I recommend spraying ACF50 inside, it's more an oil oil than a wax, and it wicks into rust very nicely, displacing any water. It won't block the drain holes either, it'll just leak out there, which is a good sign..
If your drain holes get blocked you will end up with trapped water inside the sill and that's the nightmare rust scenario.
that Anand Vaid approach looks sounds interesting but I'm not on facebook :-) (and never will be, FOMO be damned, zuck it down)
Definitely drill out the sill drain holes to at least 6mm, there are 8 holes, two at each jacking point..
https://www.miata.ne...sb/s034_94.html <- notice from mazda to drill out the sill drain holes. Doing this can also remove any existing blockage you might have. Don't worry about 'exposing metal' as part of the drilling process, having a little exposed steel for a day or two isn't a risk and it'll flash over with surface rust soon enough. The risk is water trapped inside the sill for any length of time.
What you're trying to avoid happening is this :
And why I recommend spraying something like a wicking anti-corrosion product (like ACF50) into your sills, because the product will wick into the rust and stay there, and displace any water inside/under the rust out, letting it evaporate. You end up with 'sealed' rust that can't let water get to the metal. It won't rust any more.
Thicker product like waxoyl or undersealant getting sprayed into the sill cavity would just sit on top of the rust and going 'solid' just block the drain holes. At which point any more water that gets in will cause real damage.