Transferring the cash into to buy upgrades won't affect profitability, that should still be taken into account on a monthly basis. But it will delay if not curtail cash transfers into the corporations to buy those upgrades - as that is a set benchmark.
Upgraded corporations are definitely more profitable.
Lowering taxes will also help keep cash in corporations, assuming all other things are equal.
If you are trying to maximize the cash kept in each corporation, you may also want to take a peek at the profit transfer rates. A lower rate transfers less out.
Hope that helps.
M. Ney