I began sanding about half the table top with 0000 steel wool
Just to address this point first, using steel wool is not a sanding operation and it shouldn't really be thought of as being in the same category.
The results seem quite similar but its cutting action is not the same — the action of steel wool is more akin to microscopic planing than the outright scratching from the abrasive particles bonded to the surface of sandpaper.
Should I be worried?
I don't know that you should be overly worried but yes there is the obvious concern.
For anyone unfamiliar with the subject, waterbased finishes can react with particles of steel wool trapped in the wood and they can rust, leading to tiny rust spots and subsequent dark staining if the iron reacts with tannins in the wood.
Is there anything I can do to get these steel fibers out completely?
A tack cloth might be your best removal option, but thoroughly brushing over the surface with a stiff-bristled brush, followed by wiping down with a microfibre cloth may be sufficient.
Possibly the best thing to do here would be to apply one additional coat of the Old Masters product, which with luck will successfully seal off any remaining specks of steel.
This is a personal opinion only, but since you've already used an oil-based varnish blend on the piece I don't really see why you'd choose to use a waterbased varnish on top. Using an oil-based poly as your topcoat would seem to be the ideal solution here, and it is inherently a better product (easier to apply to a high standard, stronger and more water-resistant).