You change the alpha of the minimap icons inside the options for Cartographer_Notes.
hmmm... all i see in 'Notes' are sliders for these 3:
Max minimap icons per database
Minimap icon size
i'm also having the problem with extract gas. since the nodes float around you wind up with a huge pile of them in one spot eventually, and they cover the yellow tracking dots on the minimap, rendering it much less useful. i have created my own half-transparency icons, but an option would obviously be more ideal. i believe i have the latest version (use WAU all the time).
Alright, after some research, I have concluded that Cartographer_Notes overrides all the alpha settings of any icon sent in from any module that uses it (_Herb, _ExtractGas, _Mining, etc).
What _Notes does is that for any icon that is within the minimap viewable radius (lets say this is 166.66 yards), meaning the icon is less than 166.66 yards away from you, it uses the icon at a alpha of 1.0. If the icon is off the minimap between 166.66 to 233.33 yards away (twice the distance), it draws the icon the the edge of the minimap fading away from 1.0 to 0.0 transparency the further away it is.
This is obviously by addon design, so if you want this changed, you will have to request the author of _Notes.
Meanwhile, all I can suggest is that you make the icons a lot smaller on the minimap. Alternatively, you may continue to use your own half-transparent icons, or delete all the extra nodes for every cluster of gas so you only have 1 stored node instead of 10. This would also make for a cleaner and quicker route if you used Cartographer_Routes.