I own and use an Asus Transformer with the cool reader app which works well (I am using my tablet right now to read this forum and write this reply). The primary source of headaches comes from an overly bright screen in a dark room. I tend to prefer eink over lcd, but if you are conscious of the tablet's settings then you can reduce the issues that can come up.
There are night settings that can give you a darker background and reduce the lighting. I admit to still having problems with long term use of an lcd screen, but there is no reason that a tablet can't be used as the primary reading device.
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