Have you tried batching updates? Reducing number of repaints? Most likely you can bump it to at least several thousands polygons if only you reduce the number of DOM updates.
Thinking about it, maybe a good solution (to have both a detailed map and tooltips or other contextual things) would be a canvas with precise borders, overlaid with simplified transparent SVG polygons (say, a Voronoi diagram from each polygon centroid, or something).
Take a look at OpenLayers 3. They have a few examples they use as benchmarks for canvas rendering: http://ol3js.org/en/master/examples/synthetic-lines.html http://ol3js.org/en/master/examples/synthetic-points.html
Granted, these absolutely crush Firefox (Chrome handles them fantastically; IE about average), but they're still great examples to how performant the canvas can be. As far as interactivity goes, all you need are a little bit of extra attention to your events and rendering, and it works just as well, if not better, than SVG in many cases. Look at http://ol3js.org/en/master/examples/draw-and-modify-features... for a good example.
And you're right regarding SVG overlays on a canvas - it actually works quite well: http://ol3js.org/en/master/examples/d3.html
Of course, OL3 is both highly specialized to mapping applications (you know, being mapping library and all), and highly optimized for canvas rendering, but it does serve to show flexible canvas can be.
(edit for formatting)
You can make the hidden canvas 2x larger than the visible canvas to get good precision on the borders of regions. It's admittedly hacky, but has good performance characteristics since it only uses two canvas elements.
http://bl.ocks.org/syntagmatic/6645345 (hover only activates on mousemove, so the selected region can slide off the cursor)