You do need to replace the print X's with something else when creating a line plot with raised lines. The replacement symbol you use depends upon grade level. Section 11.2 discusses design of graphics for young readers:
- For grades K-3, section 11.2.3 says that images should be shown as simple tactile shapes, rather than braille dot graphics. Furthermore, section 11.4.3 says that a solid (filled) raised shape is clearer than using a spur wheel (tooled) outline. I would take this to mean that creating X's with spurred lines is not advisable. Your suggestion of raised dots or a filled circle would work.
- For grades 4 and above, section 11.2.5 says that braille dot graphics, including full cells, may be used. However, a tactile graphic (not braille symbols) is preferred.
It is never acceptable to stack braille Xs (dots 1346) regardless of whether the number line is done with braille symbols or raised lines because of the difficulty in counting "stacked" X's (126.96.36.199).