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There is a moisture issue to consider. First, those holes are weep holes to let condensation out of the house. Since you are covering up those holes, you'll need to drill new ones above your finished patio level.
Second, I'd cover the old ones so nothing goes into the holes, and consider putting waterproofing on the brick that will be below grade so that the brick doesn't take on moisture and eventually spall from the freeze/thaw cycles.
None of this is expensive to do and is fairly easy to do during the installation process. Maybe you might never 'need' these things but I guarantee that if your house gets moldy between the brick and insulation or there are other moisture related problems later, the fix is much worse than the prevention.
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