Pen scanner
Advantages include direct interaction with the printed line, dedicated hardware, a compact form factor, standalone options on some models, a purpose-built workflow, and convenience for selective text capture.
Limitations include narrower functionality than a smartphone, a smaller screen on some devices, a learning curve for the scanning motion, and a price on top of software you may already own.
Phone
Advantages include broad ownership, a large screen, many OCR apps, a camera, cloud services, and flexible editing.
Limitations include more steps in the workflow, a camera-and-app dependency, notifications and other distractions, and a less direct interaction with the printed line.
Which should you choose?
Choose a pen scanner if you frequently scan individual words or lines and value a dedicated workflow. Choose a phone if you need broader camera, document, and software capabilities. Choose both if they serve different jobs.