this is the inherent problem with rocks on the bottom of ponds.
natural lakes etc dont have rocks. RIVERS have rocks because the fast
moving water washes the debris away.
I would:
Build a "river" going into your pond and then get in and start
removing the rocks and putting them into your stream.
Otherwise, just remove the rocks and use them decoratively elsewhere.
I got some to put on top of my lilies to keep the koi mouths out of
there (not that it worked of course).
BTW, those nooks and crannies are aerobically breaking stuff down and
that isnt great for the fish. my koi are stirring up the bottom (now
nicely strewn with the gravel that used to be in the lily pots) and
that gets sucked up by my pump and ends up in my veggie filter where I
remove it. in 7 years I have never had to clean the bottom of my
pond. I can still see the lily label on the bottom when my pond is
really clear.
Ingrid