Why's that? I use Chrome Application Shortcuts for Slack and it essentially creates a task bar shortcut, and works with desktop notifications. It's currently missing background notifications, but aside from that, there's no appreciable differences between it and something truly "native client".

Chrome on Linux is barely usable most of the time. But having something that is native lets you do all the fun things you can do with native apps: auto-start at login, minimize to systray, alt-tab with nice icon, and so on.

Maybe Slack is different, but most rich web apps I've used ends up eating gobs of memory after prolonged usage.