Both of your versions are unlikely to come up in normal speech. What you would probably say is,
He looks like a beggar.
If, as you imply, you're describing someone you met some time in the past (not just earlier today, or a day or so ago):
He looked like a beggar.
Or, more likely,
Based on the way he looked, I thought he was a beggar.
If it appears that he has given up begging,
The way he looked made me think he used to be a beggar.
Use to once meant "in the habit or custom of" but has become archaic, so that only the past tense form used to is still in common use. If you want to be more precise,
The way he looked made me think he was once a beggar.
The way you wrote it,
He looked as if he was a beggar.
This implies that you looked at him some time in the past (even just 5 minutes ago) and thought he might be a beggar, or he might not.
He looked as if he had been a beggar.
This implies that sometime in the past, he might have been a beggar, but clearly, he isn't a beggar anymore. That's the real difference between your sentences.
If you want to emphasize the ambiguity (not knowing if he was a beggar or not), try this:
His worn out clothes gave me the impression that he was a beggar.
The verb gave sets the time in the past. You might have laid eyes on him 10 minutes ago or 10 years ago, but it has already happened. Worn out clothes gives your listener an image that explains your state of mind. It explains why you thought he was a beggar.