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Thanks for choosing the Hero Me cooling system!
To your first question, I had not thought of that, but yes with the front pegs now having screw mounts, it is possible to remove the crossbar. It was easy to prototype, the files are attached. I would leave it to you to test print them and report back how it holds up while printing. ;) Note that with only two points of contact (mount) I think there will be a lot of strain on the mount pegs. I suggest that you get a 40mm threaded tube to go between the two M3 screw mounts for the tops of the 5015 fans to act as a crossbar. This gives you the clear visibility on the hot-end and some added strength to deal with rapid X movements that will otherwise stress the mount pegs.
To your second question, you may want to look at ACWest's Hero Me Dual 5015 cooling ducts. I think (the way I interpret what you mean by 'flipped around so the exhaust goes straight') that his cooling duct does what you want. https://www.thingiverse.com/thing:3481256 If not, give me a drawing (crude is fine) of what you are describing.
I will work on the Hero Me Gen3 for DD in the next couple of days. Stay tuned.