You seem to be a little confused about what function APCu performs. It only implements key/value store. It performs no opcode caching, since the whole point of APCu is to leave that to new Zend implementation of opcode.
When you use APC(u) and compatible object cache plugin WP switches to storing its cache (which is natively discarded when page load ends) and transients (which are natively stored in database) in it. While not very visible this is major change to how internals tick.
So answer to your question is two-part:
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Object cache is highly good idea since it’s used by WP big time and memory store is very very fast.
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APC(u) is just one of possible backends for object cache and if you are havving issues or concerns about it you could easily explore any alternative (memcached, redis, etc).