As of version 6.0, the option IndentPPDirectives can be used. Usage is described in this review.
Using IndentPPDirectives: None results in:
#if FOO
#if BAR
#include <foo>
#endif
#endif
While IndentPPDirectives: AfterHash gives:
#if FOO
# if BAR
# include <foo>
# endif
#endif
Edit: see @Gabriel Staples’ answer for details on the BeforeHash option introduced in clang-format version 9.