I almost always quilt around my appliques, and depending on the size of them, quilting around a part of the inside of the applique. The only time I haven't done that is on 2 quilts I did that I quilted diagonal lines both directions (diamonds) with a blending color thread, and my walking foot and quilted through everything. The first quilt was a Country Threads pattern and a combination of piecing and applique, and I like how it looked, so I did it on another quilt.
It is your quilt, and if you think it would be ok to meander over everything, go ahead and do it. No quilt police!