Mutual Identification mechanics in a deduction game
Hmmm... the best I can come up with would be need 4 types of tokens: 2 that everybody has in front of them to tell whether they are a spy or not, and 2 that are in the center of the table and tell whether each of the spies found his target. 

Everybody has two tokens (blue for spy, red for not spy) with the same background. Before the night phase, they place the fitting token in front of them (face down, ofc). Spy A awakes, looks at one of the tokens of another player. If that player was the other spy, he flips over the "spy B found" token in the center of the table. Then spy B wakes up and does the same.

There are some drawbacks:
-) you might be able to see whether tokens were moved. You can handle that the same way one night werewolf does. 

-) people need to sit very closely, so it does not work for larger groups. 

If you want larger groups you will need smartphone support or a solution that includes the spies walking around, which will very likely be very obvious.

Ps: what keeps the spies from just being very obvious about being the spies during daytime? ;)