Destiny 2 – Compatibility of Dragonfly Spec Mod with Explosive Payload Perk

Yes, the mod gets destroyed with the armor/weapon, you don't get it back.
There's no reason not to use mods on your gear though, as once you have over 280 power, you can combine mods into stronger mods and your only limiter is going to be glimmer. You can still save your best mods for raid gear though.

The Hight Impact Reserves always works like this:

The bottom half of the magazine deals extra damage, increasing as you go deeper. The final round in the magazine deals 30% extra damage.

Thanks to the research people did on Reddit (thread in question), we know that it combines with Extended Mag, but the damage cap is still at 30%:

High-Impact Reserves tops out at 30% extra damage, regardless of how many you have in the magazine. Did some testing with a Tigerspite.

Starting at 33 rounds, High-Impact Reserves will kick in when there are 16 rounds in the magazine. It hits for 108 crit damage against a Trostland level enemy on the final round.

With a Backup Mag mod, we start at 39 rounds. High-Impact Reserves kicks in when there are 19 rounds in the magazine. It also hits for 108 crit damage against a Trostland level enemy on the final round.

The benefit is that you'll see increased damage longer. Have 50 rounds? 25 will deal increased damage. Up that to 100? 50 will deal increased damage. The final round will always be the same, but you'll do more damage per magazine the bigger it is.