I think the reaction to the enemy despawns has been blown way out of proportion. I was concerned as well, but after about 25 hours of playtime, it really hasn't been an issue at all. For soul farming, your level will generally outpace your rate of soul intake by the time you eliminate an area's population. For example, I spent a while early on running a route that netted ~1200 souls per run. By the time the enemies went 'extinct', I was at an SL that required around 5000 souls to level, making that run pretty inefficient anyway. At that point, my character was also more than strong enough to handle the next 3-4 bosses.
From an item standpoint, I can see the concern, but I don't believe it's been an issue so far. I'm not sure if it's true, but I heard a rumor that enemies will drop their 'quota' before they despawn, so you should be able to collect whatever items you need before it kicks in. Even if that's not the case, it's really no different from the crystal lizards in Demon's Souls, or the Black Knights in Dark Souls.
Also, as other posters mentioned, there's always the
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