Can I accelerate Shadow Tokens with Rek'Sai Breacher?

Yes, you can accelerate Shadow Clone tokens with Rek'Sai, Breacher.

When Zed, From the Shadows resolves his "play a 0 [S] Shadow Clone unit token" ability, the token is considered "played" from a zone other than your hand, so Rek'Sai grants it Accelerate. You may pay the optional cost — 1 Energy and 1 Shadow Power — during the Pay Costs step of playing that token, and if you do, the Shadow Clone enters ready instead of exhausted.

The Shadow Clone has a single domain (Shadow/[S]), so per Rule 805.1.a.1 the Power portion must be Shadow Power — you can't use generic [A] for it. If you choose not to pay, it enters exhausted as normal.