I can give you some general pointers, and if you need any extra information, please let us know. See below:
1) Can I modify classes or plugins? Is this possible for updating?
All the code is free to modify, so please go ahead. When we release a system update, we release a full set of system files and also a patch from the previous version; you should be able to use the patch upgrade process to complete a system upgrade and retain your changes, or at the very least make your upgrade process a little easier.
2) Where can I read about updating system process?
Are you looking for information on upgrading in particular? If so, I would recommend reading docs/README in the OJS download package, and also the OJS Quick Reference, which has a fair amount of info on upgrading: http://pkp.sfu.ca/files/docs/quickrefer ... erence.pdf
2) It need to show some statistic data in some pages (pdf downloads, xml downloads, html downloads, abstract shows)
Where should I get this data? (from DB table 'articles_galley' field 'view' or something else?)
I would actually recommend looking at the existing plugins: plugins/reports/articles/, and plugins/generic/counter in particular. You may also want to take a look at how view counts are generated per galley file on the submission Editing page (the template responsible for this is templates/sectionEditor/submission/layout.tpl.