I usually alternate between stacked and unstacked when using the empire tree...your best bet is to unstack it, and then scroll to where your subverters are...you can left click on one, right click on a target, and do that for 5 or 6 of them pretty quickly, which often covers most of a fleet...

I believe the Z button, by default, quick zooms to the unit selected...I don't use defaults so I'm not sure on that, but there are available key bindings under the "Camera" section in Options -> Keybindings that allow instant zoom on the selected unit with varying degrees of how closely zoomed in you are...

There are also hotkeys (V and B?) that scroll in and out, but I think a mousewheel is still better...if the mousewheel is too slow, I'd recommend increasing the zoom sensitivity (bottom right I think on Options -> User interface)...sliding that to the right (towards green, away from red) should increase your scroll speed, which I find to be very handy...

To make things easy, its not a bad idea to group your subverters into a separate fleet...it takes a little preparation, but I have a friend who makes like 6 or 7 fleets of about 2-3 subverters each, hotkeys them to numbers (select fleet, then Ctrl + # of your choosing) and then selects them using the keyboard...if you already have a lot of fleets, that may not work out real well though...

Personally, I'd put all the subverters in a separate fleet, have them jump in a little to the left or right of your main fleet, select the fleet, and then select and attack like you have been doing already...however, if you have the fleet formation of this subverter fleet set as "loose", usually the ships will be far enough apart after they move a little bit such that you can easily click on individual ships without having to zoom in at all...

Microing subverters is a pain, but it could be worse....you could be trying to micro domina subjugators, now that is a royal pain

You can also Alt click on a subverter to select all of them and use the tab key to move through them and give individual orders to each one.  Using Tab is a lot faster than trying to find them or individually click on them in the empire tree.  Just remember, if the subverters are part of a fleet and you give an order to the flagship / fleet, you will over-ride any individual orders to subverters in that fleet.

I am not sure why it wouldn't work.  It would be hard to use if your subverters are all over the place, but it is good when a fight starts and you have a cluster of subverters.  Alt click..selects the subverters...hold shift, give a move and attack order....tab ...hold shift...give a move and attack order...tab....hold shift give a move and an attack order....repeat a few times, there done!  Is my cap dead yet?  What are my Assailants shooting at?   Meanwhile, Subverters follow their orders and break up and attack different parts of enemy fleet.  That is how I remember doing it.  Don't think I'm missing steps.

how long do subverters take to use their jump+disable ability? i tried to use it but they didn't do anything

yes, they had both the ability and the antimatter, i tried doing it again but they took so long to orient themselves towards the target (?) that it had already been destroyed before they could disable it

how long exactly does it take to "charge up"?