Your risk of these diseases is based mostly in where you will be staying. Most hotels and hostels will be perfectly safe. If you're camping or doing homestays in rural areas, your risk is higher.
Chagas can be a very serious disease in you're one of the unlucky folks that get the irreversible GI and heart problems from it. I had my own scare last summer after being bitten by a kissing bug while staying in the highlands. Thankfully, tests for the parasite came back negative. I'd rather catch dengue, malaria, and chikungunya over chagas, cause at least those are curable.
For kissing bugs, specifically, anything with DEET will help, but also take care to avoid staying in homes or buildings with thatched roofs or adobe walls. Don't sleep under palm trees if you're camping. If you want to be really safe, you can try to double up on your protection at night by using a hanging mosquito net over your bed and also sleeping inside a smaller pop-up net like this.