Overwhelmingly, the most negative effect of the Spanish incursion to Honduras was communicable diseases. The natives did not have immunity to the diseases that the Spaniards and other Europeans had built up over centuries of trade and exploration. The result was that up to 90% of native populations were wiped out.
As the Spaniards colonized Honduras, a slow process until the discovery of precious metals, they brought their culture and religion. Whether or not this is good or bad is dependent upon the view of each individual. Regardless of one's opinion, the language, culture, and religion of the Spaniards is still very evident in Honduras today. One decidedly negative effect to Honduras specifically was that a large number of the indigenous population was exported to the Caribbean to serve as slaves.
On the positive side, many new technologies, horses, cattle, and crops were introduced to Honduras.