I don't know of any specific philosophers that have written about this, but a few thoughts:
1) Are there limits on intelligence?
This seems to be the case. We live in a universe that had a distinct creation time, and which will only last a finite amount of time. Further, there are a finite number of atoms, which prevents the possibility of a created intelligent being of finite life but infinite size. So, any created being has the obvious upper bound constraint of all of time and space.
For any single being, the constraint is significantly shorter - a single person cannot use all of time and space, he or she can use at most his or her lifetime. One interesting aspect of your question is that "a created being" cannot get very far in understanding its environment - no one person has gotten very far at understanding even how to make a pencil. It is easy to forget, but much of our understanding and ability to manipulate things is due not to individual intelligence but network effects of many people.
2) Can it understand the hardware which it runs on? Yes, at least in some sense. Software can emulate/virtualize hardware. However, trying to extrapolate this to the point of your analogy, this doesn't seem knowable with respect to if we can understand the underlying "hardware"
of the universe if it turns out there is something beyond the material universe.
3) Is it possible for the program to comprehend the motives of its creator? The point of this analogy is whether humans could possibly understand the motives of some Infinite Creator or something along those lines. The analogy strikes me as interesting but of limited use: if we created a robot or computer program with some self-awareness, it would be finite just as we are. However, an Infinite Creator is infinite where we are finite. So it seems possible to build a program that understands our motives and still not be able to understand an Infinite Creator's.
4) Will it able to understand the physical world that the computer exists within? This seems very possible. It would only require sensors for detecting things in the physical world (which is easy), a method for sampling the physical world (harder, but still doable), and a way of taking observations and constructing a model of the physical world (harder still, but still possible).
By analogy, is it possible for us to understand something of the "container of this universe?" I think your analogy here is good - a computer program can only begin to understand things in the physical world for which it has sensors. Likewise, we could theoretically only understand a world beyond us to the extent we have been given the ability to sense anything about it.
5) Is it then pointless to ask the question "where do we come from"?
It seems that approaches to this question can be put into two groups:
- We can use reason to understand something of it. (e.g. Descartes)
- Reason can help, but we first must be given some help from whoever-it-is-that created us.
Approach #2 seems more common today - most people try to take their lead from data and extrapolate from that - atheists say that we have been given no evidence for anything beyond this, so that's the end of the story. Most religious groups believe that God, through revelation, has given us the needed data that supports belief in something beyond. In any case, the question itself seems useful, but depending on your perspective it might be less (for atheists) or more (for religious people) interesting.