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In our experience there are a couple of ways of doing this – on our smaller solar home systems (<50W) we now use inbuilt mounts which bolt into the rafters directly and also contain a padlock to prevent removal. The padlock is more symbolic and acts as a deterrent but seems to work.
On the larger systems the mounts and panels come with holes for threading through steel security wire which is then looped around the rafters and bolted together inside the house to prevent removal.
I know of only one case globally in our network where there was a panel theft so although there is always a concern with customers, the actually reality is very different.
We have little experience of water pumping so this would not be something I could comment on.