Not really an issue imo and the problem is more related to how well you take care of it. Imagine you'd craft like 50 weapons and never sell a single one then suddenly your inventory becomes a mess too.

To prevent your investigations becoming a mess I recommend only selecting the ones that are interesting for you and then press Start in the investigation selection screen. Start will delete all investigations that you haven't selected.

"Inventory" Management along with investigation management is kind of a nuisance but at least when it comes to the inventory, it's just the nature games that offer a lot of equipment.