tigwired,
Short answer - angle beam will yield much more meaningful results than straight beam. Straight beam will only find volumetric defects such as slag or lamination type defects in adjacent base material. Angle beam will find the slag as well as much improved detectability of lack of fusion and other throughwall type defects.
If the weld cap is not ground off, there will be little impact to the perpendicular scan, as unclesyd said, as long as the technician can start his scan far enough from the weld. The more significant impact is for the parallel scan. This scan will detect defects lying primarily across the weld. With a weld cap, all the technician can do is pass the transducer along the edge of the cap and skew the transducer to try to see under the cap.
My bottom line is to look at your materials and process and determine if there is a concern with across the weld defects (e.g. hydrogen cracking). If there is a concern, take the cap off to get full coverage. If no particular concern with across the weld defects, leave it on.
JR97