There are potential problems with shocks
and boots if the shock body is mounted
downwards. Dirt and moisture tend to
collect at the top of the shock body
with rubber/silicon boots installed,
leading to rust and pitting of the rod.
The boots are installed to protect the
rods from rock and road debris when
the shock body is mounted upwards.
With coilovers (no boots), the shock body
is typically mounted downwards and are
also mounted in locations that are more
exposed to road debris, but the springs
help to deflect the rocks. I'd venture your
longevity of the shocks would be greater
without the boots. Open to debate I'm sure.