It's been a minute since I played Jak and Daxter but I don't recall it having a map with icons littered for every Precurser Egg if it had a map at all. I've never really spent much time with Banjo but I'm guessing it's the same story. Ubisoft design their worlds so you are never more than a few moments or steps away form the next doodad to pickup. You can argue that there is more thought behind the collectables in Indy, but it's just as dense with items and as you fill out your journal, which acts much like the typical filtering system on modern in-game maps, gets littered with just as many icons. Further, you'd probably not locate a good portion of those collectables if they weren't presented as waypoints on your map or destinations markers on your HUD. A lot padding via copy and pasting can also be seen as the Vatican has you collect 15 medicine bottles throughout the area to trade in for skill books and Gizeh, the next area, ups that to 25 bottles. It's seemingly the only way to obtain those skill books and engage with those RPG-lite systems in the game. Every collectable you pickup gives you the currency you need to "learn" the skills in the skill books so as optional as they may be based on the games difficulty, skipping them would mean engaging less with thos RPG-lite systems. My may point was about density of collectables and how they are called out on your map, which is very Ubisoft-like. The pickup might have more thought put into than what you find in Ubisoft games, but those are truly open world and have different systems in place were getting something as simple as currency of loot has its' place as tedious as they become.
It's just modern design, too afraid to let players miss out on content so everything needs to be pinpointed on your map and we can't have our worlds breathe, so we have to recycle content in the game because we can't have players going more than a minute or two without stumbling upon something. This is made all the more annoying in Indy where the mapping system really doesn't feel period appropriate and further made more annoying in that the developers are obviously capable of creating interesting content as that Samson Easter Egg defies a few sins of this game as it is easy to miss and the solution is a bit of a headscratcher. Give me two or three of those per area and you can skip the hundred collectables (a good chunk being repeated from previous levels).