Is there any truth to it?
It would be important to note first the cultural difference between bathing in Malaysia and Indonesia, and the western world. In both countries, the most common form of bathing is through mandi, which utilizes a ladle water system (http://www.webcitation.org/5x2caStUE). The primary area to note in reference to the use of mandi rather than the typical poured water system associated with many other parts of the world is that there is standing water involved.
To connect to this, even today with developments in infrastructure and sanitation, Indonesia is associated with poor sanitation and water supply, with only 42.8% of households having domestic waste treatment (http://www.wepa-db.net/policies/state/indonesia/indonesia.htm). The relation between bathing in contaminated water and illness have been long documented by the World Health Organization, specifically in effects to standing water (http://www.who.int/water_sanitation_health/bathing/recreadis.pdf?ua=1). In addition, a study in 2003 demonstrated that water poured into filling collection containers were associated with higher rates of contamination, associated with accumulative buildup of pathogens in the containers themselves, even when the source of the water was found to be safe (http://www.ncbi.nlm.nih.gov/pubmed/15384721). This draws us back to the special significance to Indonesia and Malaysia, because mandi through its mechanism of use is associated with standing water.
From this point, it becomes a question of how long the water has to stand in order to become contaminated enough to cause harm to a human, and more specifically if this rate of deterioration could cause a tangible effect between water used during the day and water that may have been drawn earlier in the day. It is also important to note that in Indonesia, there is an expansive river system that, although vitally important and prolific throughout the country, are not as large or deep as others in the world such as the Huang or the Nile (http://indonesia-fascination.blogspot.com/2009/03/rivers-and-lakes-of-indonesia.html); thus, in pre-water distribution infrastructure homes, the temperature of the water used in homes would be subject to diurnal variation, which for shallow rivers as opposed to lakes or oceans can be significant (http://echo2.epfl.ch/VICAIRE/mod_2/chapt_5/main.htm). Therefore, taking a shower at night would involve water that has been standing still throughout the day, and thus has had a substantial amount of time for extra bacterial growth to take place. Thus, at a time when "common sense" local beliefs such as don't shower after 8pm came about, they would have been drawing river water in the morning and storing it throughout the day in a cool location away from the sun.
Combining these, I would posit that, because in the past populations would have drawn water in the morning to avoid diurnal variation, and that sitting water drawn from fecally contaminated sources can incubate the pathogen throughout the day, and that contaminated bathing water is associated with illness and disease, there is reason to believe that the Malaysian and Indonesian claim that taking a bath or a shower at night could cause illness has some basis in truth. This would, however, be more related to the hygiene of the water itself; its association with the time of day would be based on correlation, not causation.
As for any proposed problems outside of hygiene issues, it has been found that nighttime bathing has an effect of lowering blood pressure (http://www.ncbi.nlm.nih.gov/pubmed/16755147). This lower blood pressure can signal an underlying problem by exacerbating symptoms. So it could potentially cause a negative effect depending on the impact the bathing has on blood pressure (http://www.mayoclinic.org/diseases-conditions/low-blood-pressure/basics/symptoms/con-20032298). Apart from that, bathing in warm water is a recognized palliative treatment for rheumatoid (http://summaries.cochrane.org/CD002826/thermotherapy-heat-treatment-for-treating-rheumatoid-arthritis), and although swimming in cold water can induce pulmonary edema/adult repiratory distress syndrome (wet lung) (http://www.ncbi.nlm.nih.gov/pubmed/15302723), there were no studies available to substantiate the claim that bathing at night can result in pulmonary edema.
Beyond that, a more straightforward answer would depend on exactly what negative health effects are being considered.