Aseprite does not have full support for pens, so all a pen does is act as a way to move your cursor. There’s no support for pressure, tilt, or any other tablet features.
Because of this, using a stylus isn’t that useful in Aseprite. It’s faster for doodling and rough line sketches, but slower for precision work.
I use a Wacom Intuos tablet, but when I want to do loose sketches or block stuff in, I prefer to work in other software with pressure support, since then I can work more more fluidly and quickly than in Aseprite. I find it quicker to import my sketches into Aseprite than to have to change brush size manually while sketching.
For pixel art beyond the sketch phase, I don’t usually use the pen at all, I find it much more efficient to use the mouse.
I’m pretty used to work with a tablet (wacom intuos 2 and 3). Pen input is faster for me for most pixel work. I mapped the middle and right click on the pen’s buttons so I can pan and color pick without even using any keyboard shortcut. Zooming is a bit trickier but could be mapped to express keys.
And as eishiya said, blocking and sketching with a tablet is a must. Even if Aseprite doesn’t support pressure [EDIT: it does now!], I find the simple pen input very useful even for blocking and sketching.
I’d recommend it, even if only to give yourself a break from using a mouse all the time. Having Carpal Tunnel Syndrome will definitely impact both your speed and precision.
If this isn’t a concern I’ve always found using a mouse to be faster and more precise.
I use a drawing tablet with aseprite and I find that I get done in about an hour what used to take me half a day to do. It speeds up my workflow creatively a lot to be able to use a pen. Combined with time-saving features of aseprite like mirror-mode, and preview mode (f7 to bring up a preview window) which I use on my larger screen while I draw on the drawing tablet. This way I never have to copy-paste over and over again or zoom in and out to see how it looks… being able to see the 100% scale drawing on my main monitor while drawing on the tablet in real-time is so much better than using a mouse.