Hyperfocal distance is about having an acceptably sharp image in the depth of field. It does not mean it will be sharpest all the way through it. You still only have one distance where it actually is sharpest, and away from that, you will have reduced sharpness from defocus. If you stop down further, possibly the point of focus will be reduced in sharpness, but you might still increase the apparent sharpness at other distances, which might be more important.
If you want even closer parts of the scene in focus, you will have to stop down further.
Also the impact of diffraction softening is generally overstated. Actually try those smaller apertures and see how it affects sharpness. At f/11 compared to f/8, you will find it hard to see much difference even if you put them side by side. At f/16 it is more noticeable, but even then not significantly so.
_________________Canon DSLRs: 7D, 5D2, 1D, 600D, 450D full spectrum, 300D IR mod
Lenses: EF 35/2, 50/1.8, 85/1.8, 135/2+SF, 28-80 V, 70-300L, 100-400L, TS-E 24/3.5L, MP-E 65, EF-S 15-85 IS
3rd party: Zeiss 2/50 makro, Samyang 8mm fisheye, Sigma 150 macro, 120-300 f/2.8 OS, Celestron 1325/13
Tinies: Sony HX9V.