A mix of both.
At first traps in doujins were no different from todays twinks and pretty boys: clearly masculine features with some soft, feminine traits here and there, and always with a much "manlier" partner to increase the contrast between the two. Shota porn was just like that, except the "shota" (with an obviously adult body) was half the size of the adults.
Some years later, traps went full "draw a girl, call it a boy". No attempts to make them look masculine in the slightest were made in most cases, and since doujins back then had more genital censorship than modern ones, you could even pretend it was straight H. This trend was spread to the shota genre, but in this case the shotas at least had short hair and proportions more akin of a child.
After going from one extreme to the other, both the trap and shota artists began to depict androgyny and neoteny in a more accurate way. Traps had a chest and shoulders like men, but round hips and delicate skin like women, and their genitals were of normal size fo a man their age. Similarly, shotas had an anatomy more akin of a child, with remnants of baby fat on their faces, bellies and limbs, and their "willies" were round and cute and not adult-sized dongs or microdicks like in previous generations.
Currently, the trend for both traps and shotas is to become more and more feminine like in the 2nd era. There still are traces of masculinity in them, but western artists have been pushing trends like hyperfeminity and sissification that focus on removing men from their masculinity, and these western trends have been influencing Japanese artists too, although at a slower pace.