Consistent ID

If my links which are located at the very top of my document are "duplicated" to the very bottom of my site, how does this effect 3.2.4. My idea is basd on two sample sites:
 
1) ADA.GOV
2).DISABILITYINFO.GOV
 
The difference between the two sites is that the links at ada.gov are the very top of the page and repeated to the bottom. Disabilityinfo.gov has the links at left naviation repeated to the bottom.