MWD will give you huge speed but will drain your capacitor VERY fast. So as a result it’s more of a GTFO type of module, where you can react to a situation and either approach or bug out, but you won’t be able to have it on permanently. Except on certain T2 ships that have specific bonus to MWD usage.
Afterburner will give you less speed but its capacitor juice drain is almost negligible. As a result you can keep it permanently on.
Typically, PVP combat is very fast, lots of snap decisions and fast action, so the fight is over and you’re either dead or victorious before the MWD has had a chance to fully drain you; MWD’s are usually used in PVP combat or if you’re trying to transport something in a fast ship across a dangerous zone. Note that industrial ships (whose purpose is to transport stuff) are classified as medium-sized (cruiser-sized) but often won’t have enough powergrid to allow you to fit the 50mn (medium) MWD.
Opposite of that, PVE combat usually involves wave after wave of NPC pirates, and you have to be able to sit there and last for several long minutes; an afterburner is preferred in this case, especially if you are flying a frigate. Frigates rely on speed and mobility as their defense, esp. the ability to orbit close and fast, so for frigates the afterburner is a defense module, not just a convenience module. For slower ships (cruisers and bigger), you are supposed to rely on actual armor or shield resistances and repair to actually absorb the damage, so the afterburner becomes more of a convenience module that allows you to move around between loot cans and mission objectives.
Stealth Bombers specifically are ships that can use the Tech 2 Covert-Ops cloaking device, which lets you warp around while cloaked. With proper use of this cloaking device, you will only be vulnerable / visible at stargates, because the game forces you to have at last 1 second of visibility as you switch from the gate invisibility to your cloak’s invisibility. Also you’ll be vulnerable when you uncloak to launch your bombs; once in combat, if you get targeted, you won’t be able to re-cloak. So, basically, PVP situations, which if you get caught you’ll need the speed of a MWD to bug out / try to escape.