Not that you took issue with it but I shouldn't have said it was absurd. Not only is it an exaggeration but it's rude. Sorry about that.
One of the things that makes games like Deadlock fun is the depth to the encounters. Assassin Bebop is looking to pick people on their own, so you buy Debuff Remover and hard counter this gameplan. If Bebop is set on playing this style (and in some cases that is the right choice) then he can change his approach by making you remove one bomb but take the second using Echo Shard or abuse Debuff Remover's thrice as long+ cooldown as his hook with high mobility items to really stick to the opponent. What I'm saying is that all these potential items really help to create interactive and fun engagements. I would never, ever suggest we remove items that present counters; it was a simple miscommunication.
Having said that, Bebop's constant presence is not with his bombs. His constant presence is with his hook. It does not matter how far behind Bebop is because it's not the hook damage that matters, and it doesn't matter how hard it is to land 60m hooks when it's on an 8s cooldown with Superior Cooldown Reduction. You can't use Debuff Remover on his hook and even if you use it on his bombs, it's not like you can use it on his team. His hook singlehandedly makes Bebop a huge threat no matter what. The normal approaches to shutting down a character's primary threat are not applicable to his hook because of how safe and consistent of an ability it is.
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I want to make it clear that I would never advocate to gut his hook. It's a fun tool for picking people out of position, sniping through a team, or catching opponents during teamfights. What I don't like about his hook is that despite there being no direct counter to it save Unstoppable (which is extremely unrealistic and ridiculous to think you'd buy a 6200 item for a regular ability) and Warp Stone which has its own share of issues, and despite it being universally useful at any stage of the game and at any soul value, there's zero consequence for missing it. It's not a long cooldown, it's not detrimental to the character in any way, there's nothing. It's simply not fun to play against in its current state.
Make his hook projectile speed faster and give it a longer cooldown, transfer more power to the rest of his kit and make it a longer cooldown, make it temporarily slow him after using it, I really don't care what solution is thought of. Having oppressive bombs that you can counter play or uppercuts that deal a ton of damage or an ult that can delete people are all more engaging in a fun way to play against.