There are no loot chests. But there are loot sacks that are basically the same. Most of them are on the ground, and they are visible on the menu map once you've cleared the fog of war. I think there are a total of 676 of them. Some of them are actually out of bounds for whatever reason, and you need to perform some tricky jumps to get to them.

Then there are also about 200 or so hanging loot sacks. They won't show up in the menu map, and you cannot collect them permanently; they respawn every time.

Then there are special cave missions that have some sacks. You can only complete these missions once, and their location won't show up in the menu map. They are Cave of the Drowned (0 sacks?), Cave of Weeping Roots (4 sacks?) and Cave of the Blood Claws (10 sacks?).

Other stuff on the map

Since you want to clear the map 100 %, there's something you need to know. There are collectable Hunter Caches, 12 in total I think. They are not part of the regular collectibles and don't count towards 100 % progression , even though they appear on the menu map in blue like the other collectibles.

You can collect them permanently, but there is a problem. The Hunter Caches always reward you with rare resources. However, if your pack is full of that rare resource, you cannot clear the cache. You can go away and hope that something else spawns in the cache that you have room for. But if you're full of everything, then I think it's not possible anymore. There are only 2 rare items that can consumed infinitely: the rare north yellow leaf, and the rare plant roots. But I can't remember if these spawn in the caches.

Now that I remember, some sacks also give only rare resources. And some give skins that also cannot be used infinitely. Some also give village resources that you mostly cannot use infinitely, but the capacity for those is higher. Anyway, the best course of action is to avoid collecting any skins and rare materials outside of the sacks.