In general, do use this syntax:
sed "s/<expression>/$(command)/" file
This will look for <expression> and replace it with the output of command.
For your specific problem, you can use the following:
sed "s/0/$(date +%s)/g" input.txt > output.txt
This replaces any 0 present in the file with the output of the command date +%s. Note you need to use double quotes to make the command in $() be interpreted. Otherwise, you would get a literal $(date +%s).
If you want the file to be updated automatically, add -i to the sed command: sed -i "s/.... This is called in-place editing.
Test
Given a file with this content:
<?php return 0;
Let’s see what it returns:
$ sed "s/0/$(date +%s)/g" file
<?php return 1372175125;