The same about proving transaction inclusion: even if you hash all data, as a single SHA-256 call, then still: you can prove, that a chunk "X" is included, by giving the initialization vector, some chunks in-between, and a final SHA-256 result, for that specific chunk.
So, SPV would be of course harder, but still possible, because SHA-256 splits data into 512-bit chunks by definition.
Edit: With Merkle tree:
+---------------+------------------------------------------------------------------+
| version | 01000000 |
| prevBlockHash | 0000000000000000000000000000000000000000000000000000000000000000 |
| merkleRoot | 3ba3edfd7a7b12b27ac72c3e67768f617fc81bc3888a51323a9fb8aa4b1e5e4a |
| time | 29ab5f49 |
| difficulty | ffff001d |
| nonce | 1dac2b7c |
+---------------+------------------------------------------------------------------+
| transactions | 01 |
+---------------+------------------------------------------------------------------+
| version | 01000000 |
| inputs | 01 |
| prevTxHash | 0000000000000000000000000000000000000000000000000000000000000000 |
| prevTxId | ffffffff |
| scriptSize | 4d |
| difficulty | 04 ffff001d |
| extraNonce | 01 04 |
| genesisData | 45 |
| | 5468652054696d65732030332f4a616e2f32303039204368616e63656c6c6f72 |
| | 206f6e206272696e6b206f66207365636f6e64206261696c6f757420666f7220 |
| | 62616e6b73 |
| sequence | ffffffff |
| outputs | 01 |
| amount | 00f2052a01000000 |
| scriptSize | 43 |
| publicKey | 41 04 |
| | 678afdb0fe5548271967f1a67130b7105cd6a828e03909a67962e0ea1f61deb6 |
| | 49f6bc3f4cef38c4f35504e51ec112de5c384df7ba0b8d578a4c702b6bf11d5f |
| | ac |
| locktime | 00000000 |
+---------------+------------------------------------------------------------------+
+-----------------------+-------------------------------------+
| initialization vector | 6a09e667 bb67ae85 3c6ef372 a54ff53a |
| | 510e527f 9b05688c 1f83d9ab 5be0cd19 |
+-----------------------+-------------------------------------+
| first chunk | 01000000 00000000 00000000 00000000 |
| | 00000000 00000000 00000000 00000000 |
| | 00000000 3ba3edfd 7a7b12b2 7ac72c3e |
| | 67768f61 7fc81bc3 888a5132 3a9fb8aa |
+-----------------------+-------------------------------------+
| first hash | bc909a33 6358bff0 90ccac7d 1e59caa8 |
| | c3c8d8e9 4f0103c8 96b18736 4719f91b |
+-----------------------+-------------------------------------+
| second chunk | 4b1e5e4a 29ab5f49 ffff001d 1dac2b7c |
| | 80000000 00000000 00000000 00000000 |
| | 00000000 00000000 00000000 00000000 |
| | 00000000 00000000 00000000 00000280 |
+-----------------------+-------------------------------------+
| second hash | af42031e 805ff493 a07341e2 f74ff581 |
| | 49d22ab9 ba19f613 43e2c86c 71c5d66d |
+-----------------------+-------------------------------------+
+-----------------------+-------------------------------------+
| initialization vector | 6a09e667 bb67ae85 3c6ef372 a54ff53a |
| | 510e527f 9b05688c 1f83d9ab 5be0cd19 |
+-----------------------+-------------------------------------+
| third chunk | af42031e 805ff493 a07341e2 f74ff581 |
| | 49d22ab9 ba19f613 43e2c86c 71c5d66d |
| | 80000000 00000000 00000000 00000000 |
| | 00000000 00000000 00000000 00000100 |
+-----------------------+-------------------------------------+
| third hash | 6fe28c0a b6f1b372 c1a6a246 ae63f74f |
| | 931e8365 e15a089c 68d61900 00000000 |
+-----------------------+-------------------------------------+