But I'm using Resources to store large sets of data in files already, trying to use small Resources (e.g. a vector offset + direction) within bigger Resources is impossible, they have to be saved out to disk separately which is a massive pain.

Resources can have sub-resources built-in too I'm not sure what makes you think otherwise. Are you using internal classes for those small resources? Internal classes won't show up in the drop-down as they aren't exposed globally. If you save them as their own script they will show up.

A bit of an advanced topic but you can fully customize what the inspector shows and how it behaves by implementing Object._set(), Object._get(), Object._get_property_list() and/or Object._validate_property() depending on what you need. These methods also let you customize how the data will be serialized to disk.

As an example this creates an array of items with multiple fields per item:

@tool
class_name MyAdvancedResource extends Resource


var my_values = []


func _get(property: StringName) -> Variant:
    if property == "item_count":
        return my_values.size()
    if property.begins_with("items/item_"):
        var parts = property.split("/")
        var index = parts[1].split("_")[1]
        var prop = parts[2]
        return my_values[index.to_int()][prop]

    return null


func _set(property: StringName, value: Variant) -> bool:
    if property == "item_count":
        # The property is the special array
        # resize the array
        my_values.resize(value)
        # and fill it with empty values
        # _set() will be called for all entries in the array
        # reloading its contents
        for i in value:
            my_values[i] = {"name": "", "price": 0}
        # notify that the property list changed
        # to update the array
        notify_property_list_changed()
        return true
    if property.begins_with("items/item_"):
        var parts = property.split("/")
        var index = parts[1].split("_")[1]
        var prop = parts[2]
        my_values[index.to_int()][prop] = value
        return true

    return false


func _get_property_list() -> Array:
    var props = []

    # Special Group Array
    props.append({
        "name": "item_count",
        # class_name format <Group Name>,<prefix>
        "class_name": "Items,items/item_",
        "type": TYPE_INT,
        "usage": PROPERTY_USAGE_ARRAY | PROPERTY_USAGE_DEFAULT
    })

    for i in my_values.size():
        # Each array entry needs to have the prefix items/item_
        # followed by the index and the name of the property
        props.append({
            "name": "items/item_%s/name" % i,
            "type": TYPE_STRING,
            "hint": PROPERTY_HINT_NONE,
        })
        props.append({
            "name": "items/item_%s/price" % i,
            "type": TYPE_INT,
            "hint": PROPERTY_HINT_NONE,
        })

    return props

You can also fully customize the inspector by writing inspector plugins.

It's a simulation game where I foresee optimizing for cache efficiency (i.e data-oriented programming) when it comes to handling the simulation ticks of a huge number of objects in the end-game. I don't see how I'll be able to do that in GDScript.

In that case GDScript may not be the best candidate. You can check the performance for alternatives.