Hmm, do all the prices in InDesign have a dollar sign?
Assuming all the numbers are prices I would break this down into two searches, one for missing decimal and zeros and the other to add the ending zero.
First, finding the prices with missing decimal and zeros
Find: ^\d+(?!\.)$
Change: $0.00
The second search to add the zero to prices that already have the first number after the decimal,
Find: ^\d+\.\d$
Change $00
Please note in Change $0 is referring to a capture group (in this case this means everything found) from the Find expression and not a literal dollar sign and zero.
If the numbers do have dollar signs throughout to signify they are prices, I might tweak the Find GREPs to include the dollar sign just to make sure the GREP searches are only finding the numbers that it should be.
Before you run this on your entire document, make a copy of your file and test these out to make sure they are catching what they should. Let me know if anything needs adjusting.
Aaron