You're going to have to use judgement. There are situations where treating missing values as 0 would be insane. In general, I'd be immensely cautious.
On the other hand, there are situations where it's reasonable to attempt an alternative calculation and situations where using 0 may be reasonable.
A nice example can be found in Kenneth French's description of how Fama and French calculate book equity:
Book Equity ... is the book value of stockholders’ equity, plus balance
sheet deferred taxes and investment tax credit (if available), minus
the book value of preferred stock. Depending on availability, we use
the redemption, liquidation, or par value (in that order) to estimate
the book value of preferred stock. Stockholders’ equity is the value
reported by Moody’s or Compustat, if it is available. If not, we
measure stockholders’ equity as the book value of common equity plus
the par value of preferred stock, or the book value of assets minus
total liabilities (in that order). See Davis, Fama, and French, 2000,
“Characteristics, Covariances, and Average Returns: 1929-1997,”
Journal of Finance, for more details.
Following Fama and French, you can take a first crack at calculating book equity using the SQL code:
SEQ - COALESCE(PSTKRV, PSTKL, PSTK, 0) + COALESCE(TXDITC,0) as be
The COALESCE function returns the first non null result in the list. For the book value of preferred stock, try PSTKRV first, then PSTKL, then PSTK. Treat the tax deferred assets plus investment tax credit (TXDITC) as zero if it's unavailable.
The code here written by Palacios from CRSP and Vora from Penn State does what I described above.