It's probably because your Amiga side resolution does not match the window size on the Host system, hence the Amiga graphics output have to be scaled to fit into the window.
In the WinUAE GUI on the Settings > Host > Misc page you find several drop down lists on the right side, one of it is labeled "Graphics API". Switch that one to "Direct3D" rather than the "DirectDraw" it is by default usually.
Direct3D does usually do a smoother job on scaling than DirectDraw.
