I noticed that a lot of tablet applications including Amazon, Overstock, Wayfair and many others are using too narrow popups that are sitting in a very inconvenient zone and hard to reach with thumbs. Is it a real problem or it's so minor that UX/UI designers should not even worry about it?
It is a problem if users say it is a problem, and if these big companies haven't done something about it then I'd say that it isn't affecting their sales/transaction completion (although it is difficult to measure the impact directly). I will illustrate some points that may help you to decide how much of an issue this might be.
- I don't know if this is exactly how someone holds a tablet when they are in the context of making purchases online, but it looks like even the way the person is holding the tablet isn't that comfortable. From my experience if someone is using the tablet for a decent amount of time the device is probably going to be lying flat or propped up on an angle. In these types of configurations the user will have at least a free hand to make contact with the centre of the screen.
- The problem with designing for tablet is that even with a responsive design framework you tend to want a fixed size for modal windows because the content usually won't vary due to viewport size differences (other than the size of the font or image). So what you see as being a poor user experience is possibly the designers trying to cater for fixed content being displayed on various screen resolutions and sizes and is a compromise rather than by choice.
- It is not normally convention to align things to the left or right hand side of the screen unless it is a fixed element (e.g. navigation menus, search bars), and popups can occur potentially anywhere. Positioning things on either side of the screen would also assume a 'handedness' in how users interact with on-screen elements (disregarding whether there is left or right hand biases), so by default it should sit in the middle of the screen.