The other thing is the agent gets the entire MCP API response dumped into context as a tool response in JSON, which can be a lot. Compare that to shell commands where agents often `head` or `tail` or `grep` the response (which I kinda hate, but it does save tokens).
It also depends on whether the agent loads them on-demand or not (most modern agents do), and whether your MCP has a ton of tools or not. If your MCP only has 2 tools, and the responses aren't big, it's really not that much context.
The other thing that doesn't get talked about is the non-determinism of shell one-liners. There is a lot more non-determinism in shell tool calls; the AI can mess up commands, options, arguments. It can incorrectly filter output, miss output, miss return status, which results in re-running calls, polluting context, making results worse. Compare that to MCP calls which are more likely to succeed because they have a schema, well-defined errors, etc. Do you want less token use or more reliable results?
The thing is, you don't have to pick a side. I personally use both MCPs and CLIs at different times in different ways. Often I'll have the AI write a small script to do many calls (sometimes with tools, sometimes with libraries) which saves tokens, allows me to review, and is more deterministic.