I was also facing this in my 100% Swift project.
Whenever I added -fstack-protector-all
to the "Other C-Flags" Build Settings the flags did not show up in the binary as described in the other comments.

What I did was to create an Objective-C Class…
// DummyClassForSSP.h
#import <Foundation/Foundation.h>
NS_ASSUME_NONNULL_BEGIN
@interface DummyClassForSSP : NSObject
+ (void)dummyCallSoFlagsShowUpInIPA;
@end
NS_ASSUME_NONNULL_END
… added a dummy implementation …
// DummyClassForSSP.m
#import "DummyClassForSSP.h"
@implementation DummyClassForSSP
+ (void)dummyCallSoFlagsShowUpInIPA {}
@end
… and called it from my AppDelegate.
func application(_ application: UIApplication, didFinishLaunchingWithOptions launchOptions: [UIApplication.LaunchOptionsKey: Any]?) -> Bool {
....
DummyClassForSSP.dummyCallSoFlagsShowUpInIPA()
...
}
After that the flags showed up as described.