Re a new version of inkscape: Ninja does not force fully-correct builds, so it's on the author of the build.ninja file to either model this or not. (This is part of Ninja's objective of not mandating policy.)
To get this fully correct, note that you would need to model all inputs that Inkscape might read, which includes not only binaries but also configuration files or dynamically-loaded plugins. Some systems (I think tup?) track this by tracing executed binaries to see which file system operations they do.
Even with tracing it can be really subtle: for example if a C file has an #include "foo.h", creating a new file named foo.h earlier in the include search path is a meaningful change, which means a file-access-tracing build system also needs to track file-not-found results from previous executions.
(For C programs, also note that getting header dependencies correct includes similarly tracking all the headers in /usr/include that your program transitively includes. See the -MD vs -MMD flags to gcc.)