When I rustproofed my Seicento I didn't see any grommets anywhere, your car is an SX like my Cento so it'll have a sunroof which will be the only 3 holes along the edge of the floor/sill, I wouldn't put anything in there though as they are for the sunroof drains & tend to clog up with crud from the roads. Seicento sills aren't too bad in the corrosion department apart from at the back of the sills where it goes onto the rear arches, in this area on each side there should be a small plastic cover which is screwed on, take these off & clean/cavity wax behind them, as for the sills themselves keep them clean, polished, waxed & just keep a very close eye on them. There are a few common rust areas on the Seicento's near enough all of them are on the rear end off the car.
1) Rear arches - can be caused by general lack of keeping arches clean etc, I do mine every time I clean the Seicento just to keep an eye & keep on top of it. It could also be caused by issues which on Seicento's is a common trait as they do tend to suffer from a little incontinence
with water leakage into the boot as it comes in through either faulty rear light seals, boot seal, vent in the rear panel not sealing properly or something simple like buffers on the boot lid not aligned properly.
2) Edge of boot floor/Spare Wheel Well/Rear Panel - I've put these 3 together as where these corrode is on the edge where the panels join together, as above caused by water leaks into the boot & if ignored leads to corrosion as the water either runs down around the arches or into the edge of the floor in the spare wheel well & sits where it joins the rear panel.
3) Rear Chassis Legs/Bumper brackets - the rear legs tend to go a little flakey & if left spreads to the rear bumper brackets which are obsolete everywhere now, in fact this is the only part of the floor on the Seicento I did cavity wax inside & when the cavity wax nossle is in enough it it'll come out near the rear of the sills.
4) Front Floopan - this only happens if the sunroof drains are clogged up & it's been ignored for a long time, there are 4 small drain holes in the sunroof aperture which drain down via tubes to 6 holes on the floor edge/sill, 3 on each side, the top ones are not really an issue but the bottom ones clog up with crud resulting in blockages & water building up in the floor pans as it had nowhere to escape, it only takes minutes to just go along the edges on the floor regularly to make sure they are clear by poking something through the small holes.
So that's it's as far as I can think, I would strongly advise against drilling into any good solid bodywork as this can lead to rust, especially sills & undersides, the best thing is to regularly clean the car taking extra measure with arches, sills etc, polish & wax every so often & you should be able to keep on top of it, so when I rustproofed my Seicento I did
1) waxed whole floor pan including boot floor
2) waxed rear arches including behind protective covers on the bottom of arch
3) waxed rear chassis legs inside & out
4) waxed rear bumper brackets
5) waxed inside front arches after removing liners
6) removed rear bumper & waxed rear panel
7) general quick clean up of rear subframe whilst attached to car with wire brush & treated with rust converter.
The rustproofing took me about 2 days altogether doing it when I could after work etc, the above section with common rust areas sounds a lot worse than it actually is, it's just basically down to maintenance etc, keeping an eye on the boot/arch areas & pouncing on it as soon as you spot something starting, hope this helps.
so have left them in place at the mo.. I'll add some pics when I can, was going to ask on the FB group but posts seem to get very few comments (if any) it seems although there's a lot of members, Strange as the panda page gets loads to questions!
thanks again.
crikey,wonder how or why your hub leaked and did that, nightmare! Good job getting it sorted,worth the investment,..nice one. Is it your first Sei and have you had it long? 
