Uhm, i'm not 100% sure (didn't use that option too much either ^^), but i think those shops you already invested in appear with a white frame around the shop-symbol. So you can see in which of the 50 shops you already invested. You know
Just kiddin, i'm really not 100% sure (yet pretty sure ^^), but there ARE shops on my map that are framed like that, whereas most aren't. But maybe i misinterpreted it.
You mean the white box? I know that there are a cluster around your home base that have the white box that signifies the shop quest. And while the investment is active a box - similar to the map selection box except in a square vs. a diamond - appears around it. But after the investment times out I don't recall seeing any signifier on the map but I'll have to have another look...