I put shop as home not knowing about this when I did: http://www.webdesigner-profi.de/joomla-webdesign/joomla-shop/forum/posts/10/2398.html?lang=en
Now it's too late to move my shop from homepage for many reasons.
I have obviously the same poblem as described in the link above.
The same product linked from homepage gives me something like: www.mywebsite.com/en/shop/product1
while when linked from a lateral menu it gives me www.mywebsite.com/en/product1
Now the only solution that I found to avoid google penalization was to block the second type of links in robot.txt. But I'm not sure that's a good solution at all.
What do you suggest me to do? (please consider I can't move or remove shop from homepage nor I can remove lateral menu)