Can I publish photos or reconstructed drawing of the internal part of a patented instrument? I am doing a publication using a specific optical instrument protected by different patents. To see how it works I opened it and I have redrawn the arrangement of the optical components. Am I allow to publish my drawing for explaining the physical principle behind the measurements I have performed during my research?

It's not a reverse engineered designed, there are no specific distances between the components or other relevant details for the construction. I am showing an abstraction but more or less the parts and the arrangement is the same as the real one.

The drwaings, are of course mine. I would like to publish on my PhD thesis in Italy, but in general I am interested on any pubblication.
Following up on the answer of HairyBlob, you are also safe from copyright issues (a separate thing) if you are using your own drawings, especially if they are an abstraction of the ideas in the patent. 

There is no restriction on public discussion of patents (most places). In fact the patent process requires disclosure. But you can't republish copyright material. And your description suggests you aren't doing that.