Here is what APA describes for numbers:
Use numerals to express:
a. numbers 10 and above
examples: 12 years old, the 57th trial, 12 cm wide
b. numbers that precede a unit of measurement
examples: 5-mg dose, 36.3 mm
c. numbers that represent statistical or mathematical functions, fractional or decimal quantities, percentages, and ratios
examples: multiplied by 5, .33 of the..., more than 5% of the sample..., a ratio of 15:1
d. numbers that represent time, dates, ages, scores, points on a scale, exact sums of money and numerals
examples: 1 hr 34 min., at 3:45 am, 2-year olds, score 5 on a 12 point scale
Use numbers expressed as words:
a. when the number begins a sentence, title, or heading
examples: Forty-eight percent of the sample..., Twelve students improved...
b. common fractions
examples: one fifth of the class..., two-thirds majority
c. universally accepted language
examples: the Twelve Apostles, Five Pillars of Islam
As for percentages specifically, APA has this to say:
1. Use the percent symbol after any number expressed as a numeral. For example: 12%. In APA style, numbers greater than nine are expressed as numerals and use the percent symbol.
2. Use the word "percent" after any number expressed as a word. For example: five percent.
3. Use the word "percent" after any number that begins a sentence, title or text heading. The APA rule for numbers is that you should begin a sentence with a word even if the number is greater than nine, and the word "percent" should also be used. For example: Forty-eight percent of the sample showed an increase.
4. Use the percent symbol in tables and figures even if the symbol follows a number smaller than 10; APA style directs writers to use symbols in those cases to save space.
5. Use the word "percentage" when you do not provide an exact number. For example: The student determined the percentage of rats that ate the food in the control condition.
For more information, see the Publication Manual of the American Psychological Association.
Write out numbers beginning sentences.
Example: Six percent of the group failed.
NOT: 6% of the group failed.
https://owl.purdue.edu/owl/general_writing/grammar/writing_numbers.html
If there is a variance in why your table would not give a complete set (99% out of 100%) the topic should be address in-text, or in commentary addressing why the total is incomplete.