Normally, you should put thousands separator to improve readability.
The only guide I found (on wikipedia) is on exceptions to digit grouping where it states:
The International Bureau of Weights and Measures states that "when there are only four digits before or after the decimal marker, it is customary not to use a space to isolate a single digit". Some manuals of style state that thousands separators should not be used in normal text for numbers from 1000 to 9999 inclusive where no decimal fractional part is shown (in other words, for four-digit whole numbers), whereas others use thousand separators, and others use both. For example, the Publication Manual of the American Psychological Association stipulates a thousands separator for "most figures of 1,000 or more" except for page numbers, binary digits, temperatures, etc.
There are always common-sense exceptions to digit grouping, such as postal codes, page numbers, and ID numbers of predefined nongrouped format, which style guides usually point out.
However, the way you will present large percentages is entirely at your discretion. Percentage stands for a factor of 1/100 and you can choose to express very big percentages using it if you wish so (for example to be consistent with presentation of other values).
Also, I would not call using big percentages confusing, just harder/slower to parse.
Alternatively you can of course, drop the percentage sign and use the regular number with no factor, but this might get unnoticed if you have a bigger table, where huge percentage would visually stand out. The question is if this data is anomaly or it is the focal point of the data presented.