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java.lang.UnsatisfiedLinkError: dlopen failed: cannot locate symbol "__atomic_store_4"
Finally found solution. No need to change sqlite code. Sorry for misleading.
For armv7 I need to compile with flag: -latomic
Only now I have lots of warnings: 
./thirdparty/sqlite-3.34.0/sqlite3.c:27511:3: warning: large atomic operation may incur significant performance penalty [-Watomic-alignment]
  AtomicStore(&mem0.nearlyFull, n>0 && n<=nUsed);
./thirdparty/sqlite-3.34.0/sqlite3.c:13536:32: note: expanded from macro 'AtomicStore'
# define AtomicStore(PTR,VAL)  __atomic_store_n((PTR),(VAL),__ATOMIC_RELAXED)


But library itself functional on armv7. I think for armv7 NDK20 include only headers for atomic, but not code.