If a user clicks on a link to a t-shirt and then instead buys a pair of jeans, but no t-shirt you get the commission. Though I haven't tested it out, I'll be extremely surprised if anyone says I'm wrong on this.
The only merchant I'm aware of that differentiates between deep link sales is Amazon - they pay a higher commission if the user buys the item in the deep link and a lower commission on everything else they buy following the link.
Hard to say whether to open in a new window - this often causes a pop-up warning. Also, it depends on your site. E.g. if you have a site that's dedicated to one merchant, open it in the same window, as you have little reason to want them to return to your site once you've made the click. If your site has a lot of different stuff on it, for different merchants, you might want to open the link in a new window, in case the user wants to return to your site to check other things if they don't find what they want from the merchant.
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I used to have an open mind but my brains kept falling out.
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