The reason the bold letters look corrupted in the PDF is that the fonts do not have a true bold face. When you bold a font in Word (that doesn’t have separate bold face installed), Word bolds it by outlining the letters, thus messing it up in the PDF. Most quality fonts contain separate faces for bold (which Word automatically uses when you choose to bold the font) and those will work properly.
I am not aware offhand of fonts containing nikud which have the separate bold faces. There is a good font with nikud called Ezra SIL, but it doesn’t have a bold face.