Are good deeds superficial?

The three very basic aspects of any existence are:

1. Impermanence
2. Suffering
3. Non-Self

So the 'true nature' is also subject to these aspects. It is also impermanent and hence can change for good or bad.

It is important that one must realize these 3 aspects within oneself and not just understand them at a superficial mental level, the level of 'chintanmayi pradnya' - the one obtained by thinking, analyzing and pondering. These 3 aspects must be realized at the level of experience, the level of 'bhavanamayi pradnya' - experiential wisdom, which is gained through meditation.

Assuming one needs to change the 'true nature' for good, i.e. become less agitated, less lustful etc. Any true change can only come about when we change the way our unconscious mind works. This is only possible when we have access to the unconscious mind. For that one needs 'concentration'. But concentration is antithetical to an agitated mind, to a lustful mind. Hence to gain concentration, one needs to practice 'morality' - one must try to keep the five precepts in daily life. One must try to do good deeds. With morality and concentration, one is able to develop 'wisdom' - which will take us to final liberation.

So you ask, 'So can we change our 'true nature' by just doing good deeds? Or good deeds have to come from our true nature?' Initially one must start by doing good deeds, keeping precepts. But one must graduate to meditation (start by going to a meditation retreat) to develop concentration and wisdom, so that every deed we perform is beneficial for us and others.

Good deeds help to develop and maintain wholesome mind states which is a very important part of Right Effort and can lead all the way to the stage of stream entry.

A great in depth resource for understanding the benefit of our good deeds to ourselves is Merit: A Study Guide by Thanissaro Bhikkhu. From the intro:

Of all the concepts central to Buddhism, merit (puñña) is one of the least known and least appreciated in the West. This is perhaps because the pursuit of merit seems to be a lowly practice, focused on getting and "selfing," whereas higher Buddhist practice focuses on letting go, particularly of any sense of self. Because we in the West often feel pressed for time, we don't want to waste our time on lowly practices, and instead want to go straight to the higher levels. Yet the Buddha repeatedly warns that the higher levels cannot be practiced in a stable manner unless they develop on a strong foundation. The pursuit of merit provides that foundation. To paraphrase a modern Buddhist psychologist, one cannot wisely let go of one's sense of self until one has developed a wise sense of self. The pursuit of merit is the Buddhist way to develop a wise sense of self.

and

The section on merit then sets out in general terms the types of meritorious activities that conduce to that happiness, focusing primarily on three: giving, virtue, and meditation.

and

All three of these forms of merit conduce to the highest form of merit: the realization of stream-entry, the first glimpse of the deathless. Thus the penultimate section of this study guide focuses on the happiness and well-being that derive from this attainment.

There is definitely an understanding that keeping your mind on doing good deeds is beneficial and important and can lead to the attainment of Sotāpanna; which is not a superficial change.

I am going to give you an answer from an Abhidhamma perspective.

What happens to us arises because of kamma and many other conditions.

There is no “decider” to determine the reaction (wholesome or unwholesome) to what happens, but a decision is made naturally (without a “decider”). The decision is a natural result of defilements / accumulations / habits / pārami / vows / tendencies / the environment / your mood / recent events. The mechanism by which the decision is made is called “natural decisive support condition” (pakatūpanissayapaccaya).

The intensity of the volition associated with the reaction (and therefore the weightiness of the kamma produced) and the intensity of the other mental factors (how strong the attachment, the amount of compassion, etc.) is also determined by “natural decisive support condition”.

I know that “natural decisive support condition” sounds like a healthcare product :-), but it is a very important concept at the heart of the strategy to spiritual development. The cause (conditioning state) of “natural decisive support condition” is something “strong” that happened in the past (mental state, sensed object or idea). The result (conditioned state) of “natural decisive support condition” is the current mental state (all mental states).

So when good things are done repeatedly, this creates a “strong” past conditioning state (strong because of repetition) that will naturally influence future decisions and the weightiness of the future kamma produced. This is why we undertake “rules of training” (precepts). This is why the Buddha talked of “training” monks (see MN 107). The mind cannot be controlled, but it can be trained. One should approach spiritual development with a training paradigm, not a control paradigm.

Training the mind is like any type of training. It is not a “control" paradigm, it is a “working with" approach. The mind is like a little puppy dog, it cannot be controlled but it can be trained. It requires patience, repetition, patience, energy, patience, commitment, patience and consistency. It also takes a lot of patience!

So to answer your specific question... wholesome deeds performed in the past condition present wholesome deeds through “natural decisive support condition”. Unwholesome deeds performed in the past condition present unwholesome deeds through “natural decisive support condition”.

Doing good deeds is very beneficial because our moral character is changeable. When we do good deeds, our moral character improves. When we do bad deeds, our character worsens.

However, according to the Buddha's teaching of dependent origination, the ultimate cause of all our negative qualities is much deeper than that. This underlying root cause is ignorance, so the only way to permanently change is to overcome ignorance. To do good deeds without overcoming ignorance is very good, but it isn't enough to become enlightened.

To overcome ignorance, one must develop wisdom by developing insight into the nature of reality. Once this wisdom is attained and brought to perfection, the ignorance that is the underlying cause of all suffering is brought to an end.