You can activate Color Cell by value to highlight missing values :
Unfortunately, even if the user doesn't specify colors for the other values, JMP will use some color scale automatically.
This is why this code
Names Default to Here(1);
dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt[[5,7,9,12],{height}]=999;
:height <<
Set Property( "Missing Value Codes", {999} ) <<
Set Property(
"Value Colors",
{999 = "Medium Light Gray", Color Cell by Value( 1 )}
)
produces this view:

You can use one of these workarounds to get transparent missing values - without affecting the other cells:
- set all the other values to white

use color gradient (from white to white):
:height << Set Property( "Missing Value Codes", {999} ) <<
Set Property(
"Color Gradient",
{{"white", {"Continuous", "Categorical", "Diverging"}, {{255, 255, 255},
{255, 255, 255}, Missing( "Black" )}}, Range( {0, 50, 100} ),
Color Cell by Value}
)