I think you've misunderstood something. sq has no problem generating certificates with subkeys. Here's the default structure. Notice that we actually include a separate signing subkey by default. This makes it harder to use a data signature where e.g. a self signature is expected and vice verse. This can help protect against some collision attacks, among others.

  $ sq key generate -u '<alice@example.org>' --export /tmp/alice.pgp; sq inspect /tmp/alice.pgp
  /tmp/alice.pgp: Transferable Secret Key.
  
      Fingerprint: 99E2 68B5 F5A2 45E9 4A9F  A1FB F10A BDD2 C1BC 2478
  Public-key algo: EdDSA Edwards-curve Digital Signature Algorithm
  Public-key size: 256 bits
       Secret key: Unencrypted
    Creation time: 2021-02-15 21:34:45 UTC
  Expiration time: 2024-02-16 15:01:06 UTC (creation time + P1095DT62781S)
        Key flags: certification
  
           Subkey: E54F CB2B 4619 FDB9 680A  974C 94D7 9D77 395B 8A7C
  Public-key algo: EdDSA Edwards-curve Digital Signature Algorithm
  Public-key size: 256 bits
       Secret key: Unencrypted
    Creation time: 2021-02-15 21:34:45 UTC
  Expiration time: 2024-02-16 15:01:06 UTC (creation time + P1095DT62781S)
        Key flags: signing
  
           Subkey: 62BF 9E6B C022 D3FB 681F  5279 2B09 341C EDFE 0AF9
  Public-key algo: ECDH public key algorithm
  Public-key size: 256 bits
       Secret key: Unencrypted
    Creation time: 2021-02-15 21:34:45 UTC
  Expiration time: 2024-02-16 15:01:06 UTC (creation time + P1095DT62781S)
        Key flags: transport encryption, data-at-rest encryption
  
           UserID: <alice@example.org>