when I say A affects B, does it imply that A has a negative effect on B?
Sunshine affects my mood.
That sentence is entirely neutral; it's impossible to say whether I feel better or worse in sunshine. One might assume that I enjoy it, or perhaps it exacerbates a skin condition. You can't tell.
Very often there is enough context to determine whether the effect of A on B is positive or negative...
Sunshine affects my mood. I'm always smiling.
Sunshine affects my mood. I try to stay indoors.
...but the context is necessary. The initial sentence on its own is not enough.
It would be sensible to define your terms. Which sense of imply would you like us to guess you're using (imply 2. (Logic) to suggest or involve as a necessary consequence [Collins])?
The best ways to investigate this sort of claim do include looking in decent dictionaries.
Compare the first-given (and in a non-historical dictionary, this indicates frequency of this sense being the intended one) definitions for the transitive usage/s at AHDEL, Collins and RHK Webster's:
.1. To have an influence on or effect a change in: Inflation affects the buying power of the dollar. [AHDEL]
.1. to act upon or influence, esp in an adverse way: damp affected the sparking plugs.[Collins]
.1. to produce an effect or change in: Cold weather affected the crops.[RHK Webster's]
So there is at least a connotation of a negative (in the sense of adverse) effect. The Collins definition pushes this reasonably close to denotation, but it's probably justifiable to average these analyses to get a general picture.
This is doubtless compounded by the most usual sense of the homonym:
affect 1. To put on a false show of; simulate [AHDEL]
This is not to say that these vibes will be picked up identically by all people, and certainly not in all contexts (The mass of a planet will obviously affect its gravity).
Maybe my view is contrarian to the ones here. Yes I do think 'affect' has a negative connotation. To start with 'effect' is a noun and 'affect' is a verb. Effect is usually qualified (with an adjective) to give a +ve or -ve connotation eg. Lack of regular sleep could have a detrimental effect on your studies. 'Sunshine affects my mood' is not a common usage like say 'gloomy weather affects my mood' and obviously it puts a -ve connotation. While one can use say 'spur' to indicate a +ve effective - for eg, morning jog spurs me to start the day on a bright note. At the same, for eg, A lengthy meeting or discussions affects my schedule - it can be read in only one way (-ve). To summarize, I think effect has a neutral, if not +ve, ring to it while affect has a -ve ring to it.
AFFECT does not connote either negative or positive result, "affect" merely indicates that something influenced or caused some response or change in another person/object/event. The further details you provide will "affect" or determine whether or not the import of your expression is understood as negative or positive.
What follows are the first 4 results I encountered on a keyword search of AFFECT (note: these definitions are not cherry-picked to support my position. I'm sure you will find just as many dictionaries that disagree with my contention.)
AFFECT (verb): 1. the conscious subjective aspect of feeling or emotion; 2. affect, impact, bear upon, bear on, touch on, touch; (verb) have an effect upon. "Will the new rules affect me."; 3. affect (verb): act physically on; have an effect upon. “the medicine affects my heart rate" 4. Involve, affect, regard (verb) connect closely and often incriminatingly. "This new ruling affects your business"; 5. feign, sham, pretend, affect, dissemble (verb): make believe with the intent** to deceive "He feigned that he was ill"; "He shammed a headache" 6. affect, impress, move, strike (verb): have an emotional or cognitive impact upon “This child impressed me as unusually mature”; This behavior struck me as odd” Definitions.net
AFFECT (verb): 1. to act upon; to produce an effect or change upon; 2. affect (verb): to influence or move, as the feelings or passions; to touch; 3. affect (verb): to love; to regard with affection; 4. affect (verb): to show a fondness for; to like to use or practice; to choose; hence, to frequent habitually; 5. affect (verb): to dispose or incline; 6. affect (verb): to aim at; to aspire; to covet; 7. affect (verb): to tend to by affinity or disposition; 8. affect (verb) to make a show of; to put on a pretense of; to feign; to affect ignorance; 9. affect (verb): to assign; to appoint; 10. affect (noun): affection; inclination; passion; feeling; disposition. Webster Dictionary
AFFECT (verb): affect; 3rd person present: affects; past tense: affected; past participle: affected; gerund or present participle: affecting
have an effect on; make a difference to. "the dampness began to affect my health" synonyms: have an effect on, influence, act on, work on, have an impact on, impact;
1:obsolete : feeling, affection
2: the conscious subjective aspect of an emotion considered apart from bodily changes; also: a set of observable manifestations of a subjectively experienced emotion (patients … showed perfectly normal reactions and affects—Oliver Sacks)