UPDATE: No longer needed in WP 5.9 // Fixes Bug #51612 in WordPress Core where block filters (pre_render_block and render_block_data) only get called for top level blocks (not for innerBlocks/nested)

block-editor.php

<?php
// phpcs:ignoreFile PSR1.Files.SideEffects

namespace CoreFunctionality\BlockEditor;

/**
 * Fixes Bug #51612 in WordPress Core
 *  where block filters (pre_render_block and render_block_data)
 *  only get called for top level blocks (not for innerBlocks/nested)
 *
 * Current Workaround is to hook into render_block_data
 *  and render each innerBlock (recursively) with render_block
 *  because core doesn't use render_block for innerBlocks but only WP_Block::render
 *  but pre_render_block and render_block_data only get called in render_block
 *
 * Changes in render_block/WP_Block have to be monitored and maybe this won't be required in future
 *
 * @see https://core.trac.wordpress.org/ticket/51612
 */
class BlockFilterWorkaround
{
    public function __construct()
    {
        /**
         * hook latest possible priority (= PHP_INT_MAX) so other hooks which change data run first
         * our function doesn't change data, it only renders innerBlocks and stores them
         */
        add_filter('render_block_data', [$this, 'render_block_data'], PHP_INT_MAX, 2);
    }

    /**
     * Callback for `render_block_data`
     *
     * @see wp-includes/blocks.php:687
     * @param array $block
     * @param array $sourceBlock
     * @return array filtered block data with rendered inner blocks
     */
    public function render_block_data($block, $sourceBlock) // phpcs:ignore PSR1.Methods.CamelCapsMethodName
    {
        // only run if has innerBlocks, maximum nested block without innerBlocks just returns data
        if (isset($block['innerBlocks']) && $block['innerBlocks']) {
            $renderedInnerBlocks = [];
            /**
             * call render_block foreach innerBlock
             * this calls pre_render_block and render_block_data for nested blocks
             * calling render_block_data on a nested block also
             *  calls this method again recursively (for inner-innerBlocks)
             */
            foreach ($block['innerBlocks'] as $i => $innerBlock) {
                $renderedInnerBlocks[] = render_block($innerBlock);
            }

            $innerBlockIndex = 0;

            /**
             * on WP_Block::render it checks for all chunks of innerContent
             *  and if any of these chunks is a string it outputs that string
             *  instead of calling render on the inner block
             * see class-wp-block.php::208-212
             */
            foreach ($block['innerContent'] as $i => $innerContent) {
                /**
                 * innerContent has structure of [wrapperDiv, null, endDiv] for most blocks
                 *  therefore only put values in the "null" elements
                 *  see class-wp-block.php::208-212
                 */
                if (!is_string($innerContent)) {
                    $block['innerContent'][$i] = $renderedInnerBlocks[$innerBlockIndex++];
                }
            }
        }

        return $block;
    }
}

new BlockFilterWorkaround();

See https://core.trac.wordpress.org/ticket/51612

UPDATE: WordPress 5.9 includes a bug fix, so this workaround is no longer required.
See https://core.trac.wordpress.org/ticket/51612