Why Use a Scanner App
If you use a camera rather than a phone, you will want to know about Tropy. Tropy is a photo management tool for archival research. You take photos on your camera (JPEGs) and Tropy can help you to organize and take notes on them. Tropy is excellent for quick research trips in which you amass huge numbers of photos, but you don't have a plan on how you will be using them. It is especially useful for manuscript materials that are handwritten and will require some transcription. (PDFs/ scanner app might be better if you are mostly photographing typewritten materials). See the tab on Tropy for more information.
No matter what you use, find a system for keeping track of your images.
If you are mostly taking images to quickly acquire text documents for research at a later time, your scanner app is probably the easiest way.
Remember that cameras (including your phone camera) take single images and they are stored as large files (JPEGs). You will have to take time to convert them to usable form, and then recombine them into single files. Try to weigh that against the time it would take to just take the time to read and take good notes.
Scanner apps will create multi-page PDFs. You could create an organization scheme where every archival folder or document can be in a single document which you can then instantly upload to the cloud. Your PDFs don't have to go through another application to be edited or resized. Some scanner apps will automatically run OCR (Optical Character Recognition) as well so that typed text will be searchable.
If you are taking images of photographs, blueprints, maps, or other illustrations and you want the highest resolution possible, a good camera image is probably better. And if you truly want publication-quality images, you might just want to pay for the on-site services of bigger institutions who have professionally-trained staff, overhead cameras, flatbed scanners, and other far superior tools for the best images.
Other positives: Automatically backs up to the cloud on their server, so you don't have to do anything extra to move to the cloud.
Downsides: Once you have completed a document, it isn't as easy to add a new page as it in JotNot.