What are the differences between red and blue containers?

Items highlighted in blue are containers or trap triggers and need to be activated "by hand", that is, you must approach them to activate them. They also cannot be destroyed.

Items highlighted in red can be destroyed or activated by shooting at them, and are either containers, traps, or used by monsters for buffs. These items can also be used for destroyed object bonuses, along with other destructible items such as tomb stones, tables, etc. This latter group never contains anything which is why they aren't highlighted.

Red highlight means it's a destructible object while blue is usually a container for items. Therefore dead villagers will also not count for destroyed object bonuses.